git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@27 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/Makefile

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+# Makefile for serial tools
+
+#
+# Targets
+#
+
+all:
+	$(MAKE) binary2txt replicate restart2data chain micelle2d data2xmovie
+
+binary2txt:	binary2txt.o
+	g++ -g binary2txt.o -o binary2txt
+
+replicate:	replicate.o
+	g++ -g replicate.o -o replicate
+
+restart2data:	restart2data.o
+	g++ -g restart2data.o -o restart2data
+
+chain:	chain.o
+	ifort chain.o -o chain
+
+micelle2d:	micelle2d.o
+	ifort micelle2d.o -o micelle2d
+
+data2xmovie:	data2xmovie.o
+	g++ -g data2xmovie.o -o data2xmovie
+
+clean:
+	rm binary2txt replicate restart2data chain micelle2d data2xmovie
+	rm *.o
+
+#
+# Rules
+#
+
+.cpp.o:
+	g++ -g -c $<
+
+.c.o:
+	gcc -g -c $<
+
+.f.o:	
+	ifort -O -w -c $<

tools/README

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+LAMMPS pre- and post-processing tools
+
+This directory contains several stand-alone tools for creating LAMMPS
+input files and massaging LAMMPS output data.  Instructions on how to
+use the tools are discussed in the Tools section of the LAMMPS
+documentation.  The source files in this directory have additional
+comments that may be useful at the top of the code.  The packages that
+reside in their own sub-directories have README files of their own
+that you want to look at.
+
+You will need to compile each of these tools if you wish to use them.
+Building LAMMPS itself (in the src dir) does not build these tools.
+
+These are the included tools:
+
+binary2txt	       convert a LAMMPS dump file from binary to ASCII text
+replicate	       replicate a LAMMPS data file in one or more dimensions
+restart2data	       convert a binary restart file to an input data file
+data2xmovie	       convert a data file to a snapshot that xmovie can viz
+chain		       create a data file of bead-spring chains
+micelle2d	       create a data file of small lipid chains in solvent
+
+xmovie		       a quick/simple viz package that displays 2d projections
+			 of 3d LAMMPS snapshots
+
+amber2lammps	       python scripts for using AMBER to setup LAMMPS input
+ch2lmp		       convert CHARMM files to LAMMPS input
+lmp2arc		       convert LAMMPS output to Accelrys Insight format
+		         for analysis
+lmp2cfg		       convert LAMMPS output to CFG files that can be
+		         read by AtomEye visualizer
+lmp2traj	       convert LAMMPS output to contour, density profiles 
+msi2lmp		       use the Accelrys Insight (nee MSI/Biosym Discover)
+		         code to setup LAMMPS input
+
+The set of tools are single C, C++, or Fortran files.  A Makefile for
+building them is included in this directory, but you will have to edit
+it for the compilers and paths on your system.
+
+The other tools are in their own sub-directories, and each has its own
+README file on how to build and use it.

tools/amber2lmp/README

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+These Python scripts were written originally by Keir Novik, but he can
+no longer support them.  See some documentation at the top of the
+files - they are supposed to be fairly self-explanatory.
+
+amber2lammps.py		converts AMBER files into LAMMPS input format
+dump2trj.py		converts LAMMPS dump files into AMBER format
+dump2try99.py		same as dump2trj for LAMMPS 99 format
+
+-------------------------
+
+Modifications in file amber2lammps.py, by Vikas Varshney
+Dated July 5, 2005
+Email address : vv5@uakron.edu
+
+Lines 222-226: Undid the shifting of the atoms in the periodic
+box. LAMMPS is going to take care of it by image atoms. Make sure that
+when you dump the coordinates by LAMMPS to view in VMD, print them in
+the format mentioned in the dump2ptraj.py section later.
+
+Lines 378-391: Added an if statement to see whether .crd or .top file
+is being read. This if statement helps in assigning the title if the
+title is not present in the files.
+
+Line 394: Added an if statement, not to read lines which start with
+% in the topology file.
+
+Lines 430-432: Changed if statement condition to read the current
+simulation time from .crd file. I put the remainder condition
+instead of equal to condition. The simulation time adds one value to
+the length of the Item_list, so remainder condition can be applied
+easily to see if simulation time data is present in the .crd file or
+not.
+
+In general, the initial .crd files dont have simulation time
+information while restart files do have them.
+
+Some other minor additions: 
+
+I added few lines to print the names which are being read
+currently. This helps in seeing current state of the programs which
+are listed below
+
+Lines 382, 389, 420, 428, 436, 490, 498, 550, 555, 560, 565, 570, 575,
+580, 595, 600, 610, 615, 620, 631, 636, 648, 657, 666, 677, 688, 701,
+720, 725, 730, 735, 740, 745, 750, 755, 767, 769, 771, 778, 785, 806,
+821, 897.
+
+---------------------------
+
+Modifications in file dump2trj.py, by Vikas Varshney
+Dated July 5, 2005
+Email address: vv5@uakron.edu
+
+First, the atoms should be dumped in the following format.
+
+dump group-ID custom N tag type xs ys zs ix iy iz
+
+Modifications:
+
+Lines 117-119: I modified the lines to get the actual co-ordinates
+instead of box coordinates. If we dont do that and try to see the
+file in vmd, we observe long bond lengths of the molecules whose one
+part is on one side of periodic box and the other part is on other
+side of periodic box.
+
+Lines 239 & 244: Changed x to mdcrd.
+
+Once you do that. Open the original topology file in VMD (with parm7)
+and then mdcrd file (crdbox) to see the time evaluation of the
+problem.
+
+----------------------------
+
+Example input script, by Paul Crozier
+1 Sept 2005
+
+Here is an example of a typical LAMMPS input script for use with 
+a data file built by amber2lammps.py:
+
+units			real
+neigh_modify    delay 5 every 1
+atom_style		full
+bond_style      harmonic
+angle_style     harmonic
+dihedral_style  harmonic
+pair_style      lj/cut/coul/long 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+read_data       data.yourdata
+fix             1 all nve
+special_bonds   amber                               
+thermo          1
+thermo_style    multi
+timestep        0.5
+run             2

tools/amber2lmp/amber2lammps.py

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+#! /usr/bin/python
+
+#
+# This is amber2lammps, a program written by Keir E. Novik to convert
+# Amber files to Lammps files.
+#
+# Copyright 1999, 2000 Keir E. Novik; all rights reserved.
+# 
+# Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README
+#
+
+#============================================================
+
+def Pop(S, I=-1):
+    'Pop item I from list'
+    X = S[I]
+    del S[I]
+    return X
+
+#============================================================
+
+class Lammps:
+
+    #--------------------------------------------------------
+
+    def Dump(self):
+        'Write out contents of self (intended for debugging)'
+        Name_list = self.__dict__.keys()
+        Name_list.sort()
+        for Name in Name_list:
+            print Name + ':', self.__dict__[Name]
+
+    #--------------------------------------------------------
+
+    def Write_data(self, Basename, Item_list):
+        'Write the Lammps data to file (used by Write_Lammps)'
+        import os, sys
+
+        Filename = 'data.' + Basename
+
+        Dir_list = os.listdir('.')
+        i = 1
+        while Filename in Dir_list:
+            Filename = 'data' + `i` + '.' + Basename
+            i = i +1
+        del i
+
+        print 'Writing', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename, 'w')
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return
+
+        try:
+            F.writelines(Item_list)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+        F.close()
+        print 'done.'
+
+    #--------------------------------------------------------
+
+    def Write_Lammps(self, Basename):
+        'Write the Lammps data file, ignoring blank sections'
+        import string
+        L = []
+
+        L.append('LAMMPS data file for ' + self.name + '\n\n')
+
+        L.append(`self.atoms` + ' atoms\n')
+        L.append(`self.bonds` + ' bonds\n')
+        L.append(`self.angles` + ' angles\n')
+        L.append(`self.dihedrals` + ' dihedrals\n')
+        L.append(`self.impropers` + ' impropers\n\n')
+
+        L.append(`self.atom_types` + ' atom types\n')
+	if self.bonds > 0:
+            L.append(`self.bond_types` + ' bond types\n')
+	if self.angles > 0:
+            L.append(`self.angle_types` + ' angle types\n')
+	if self.dihedrals > 0:
+            L.append(`self.dihedral_types` + ' dihedral types\n')
+	L.append('\n')
+        
+        L.append(`self.xlo` + ' ' + `self.xhi` + ' xlo xhi\n')
+        L.append(`self.ylo` + ' ' + `self.yhi` + ' ylo yhi\n')
+        L.append(`self.zlo` + ' ' + `self.zhi` + ' zlo zhi\n\n')
+
+        if self.atom_types != 0:
+            L.append('Masses\n\n')
+            for i in range(self.atom_types):
+                L.append(`i+1` + ' ' + `self.Masses[i]` + '\n')
+            L.append('\n')
+
+            L.append('Pair Coeffs\n\n')
+            for i in range(self.atom_types):
+                L.append(`i+1`)
+                for j in range(len(self.Nonbond_Coeffs[0])):
+                    L.append(' ' + `self.Nonbond_Coeffs[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.bonds != 0 and self.bond_types != 0:
+            L.append('Bond Coeffs\n\n')
+            for i in range(self.bond_types):
+                L.append(`i+1`)
+                for j in range(len(self.Bond_Coeffs[0])):
+                    L.append(' ' + `self.Bond_Coeffs[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.angles != 0 and self.angle_types != 0:
+            L.append('Angle Coeffs\n\n')
+            for i in range(self.angle_types):
+                L.append(`i+1`)
+                for j in range(len(self.Angle_Coeffs[0])):
+                    L.append(' ' + `self.Angle_Coeffs[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.dihedrals != 0 and self.dihedral_types != 0:
+            L.append('Dihedral Coeffs\n\n')
+            for i in range(self.dihedral_types):
+                L.append(`i+1`)
+                for j in range(len(self.Dihedral_Coeffs[0])):
+                    L.append(' ' + `self.Dihedral_Coeffs[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.atoms != 0:
+            L.append('Atoms\n\n')
+            for i in range(self.atoms):
+                L.append(`i+1`)
+                for j in range(len(self.Atoms[0])):
+                    L.append(' ' + `self.Atoms[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.bonds != 0 and self.bond_types != 0:
+            L.append('Bonds\n\n')
+            for i in range(self.bonds):
+                L.append(`i+1`)
+                for j in range(len(self.Bonds[0])):
+                    L.append(' ' + `self.Bonds[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.angles != 0 and self.angle_types != 0:
+            L.append('Angles\n\n')
+            for i in range(self.angles):
+                L.append(`i+1`)
+                for j in range(len(self.Angles[0])):
+                    L.append(' ' + `self.Angles[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        if self.dihedrals != 0 and self.dihedral_types != 0:
+            L.append('Dihedrals\n\n')
+            for i in range(self.dihedrals):
+                L.append(`i+1`)
+                for j in range(len(self.Dihedrals[0])):
+                    L.append(' ' + `self.Dihedrals[i][j]`)
+                L.append('\n')
+            L.append('\n')
+
+        self.Write_data(Basename, L)
+
+#============================================================
+
+class Amber:
+    def __init__(self):
+        'Initialise the Amber class'
+        self.CRD_is_read = 0
+        self.TOP_is_read = 0
+
+    #--------------------------------------------------------
+
+    def Dump(self):
+        'Write out contents of self (intended for debugging)'
+        Name_list = self.__dict__.keys()
+        Name_list.sort()
+        for Name in Name_list:
+            print Name + ':', self.__dict__[Name]
+
+    #--------------------------------------------------------
+
+    def Coerce_to_Lammps(self):
+        'Return the Amber data converted to Lammps format'
+
+        import math
+
+        if self.CRD_is_read and self.TOP_is_read:
+            l = Lammps()
+            print 'Converting...',
+
+            l.name = self.ITITL
+            l.atoms = self.NATOM
+            l.bonds = self.NBONH + self.MBONA
+            l.angles = self.NTHETH + self.MTHETA
+            l.dihedrals = self.NPHIH + self.MPHIA
+            l.impropers = 0
+            l.atom_types = self.NTYPES
+            l.bond_types = self.NUMBND
+            l.angle_types = self.NUMANG
+            l.dihedral_types = self.NPTRA
+
+            Shift = 0
+            if self.__dict__.has_key('BOX'):
+                l.xlo = 0.0
+                l.xhi = self.BOX[0]
+                l.ylo = 0.0
+                l.yhi = self.BOX[1]
+                l.zlo = 0.0
+                l.zhi = self.BOX[2]
+                if (l.xlo > min(self.X)) or (l.xhi < max(self.X)) or \
+                   (l.ylo > min(self.Y)) or (l.yhi < max(self.Y)) or \
+                   (l.zlo > min(self.Z)) or (l.zhi < max(self.Z)):
+                    #  Vikas Modification: Disabling Shifting. This means I am intend to send exact coordinates of each atom and let LAMMPS 
+                    #  take care of imaging into periodic image cells. If one wants to shift all atoms in the periodic box, 
+                    #  please uncomment the below 2 lines.
+	            print '(warning: Currently not shifting the atoms to the periodic box)' 
+                    #Shift = 1
+            else:
+                print '(warning: Guessing at periodic box!)',
+                l.xlo = min(self.X)
+                l.xhi = max(self.X)
+                l.ylo = min(self.Y)
+                l.yhi = max(self.Y)
+                l.zlo = min(self.Z)
+                l.zhi = max(self.Z)
+
+            # This doesn't check duplicate values
+            l.Masses = []
+            for i in range(l.atom_types):
+                l.Masses.append(0)
+            for i in range(self.NATOM):
+                l.Masses[self.IAC[i] - 1] = self.AMASS[i]
+
+            l.Nonbond_Coeffs = []
+            for i in range(self.NTYPES):
+                l.Nonbond_Coeffs.append([0,0])
+            for i in range(self.NTYPES):
+                j = self.ICO[i * (self.NTYPES + 1)] - 1
+                if self.CN1[j] == 0.0:
+                    l.Nonbond_Coeffs[i][0] = 0.0
+                else:
+                    l.Nonbond_Coeffs[i][0] = \
+                                0.25 * (self.CN2[j])**2 / self.CN1[j]
+                if self.CN2[j] == 0.0:
+                    l.Nonbond_Coeffs[i][1] = 0.0
+                else:
+                    l.Nonbond_Coeffs[i][1] = \
+                                (self.CN1[j] / self.CN2[j])**(1.0/6.0)
+
+            l.Bond_Coeffs = []
+            for i in range(self.NUMBND):
+                l.Bond_Coeffs.append([0,0])
+            for i in range(self.NUMBND):
+                l.Bond_Coeffs[i][0] = self.RK[i]
+                l.Bond_Coeffs[i][1] = self.REQ[i]
+
+            l.Angle_Coeffs = []
+            for i in range(self.NUMANG):
+                l.Angle_Coeffs.append([0,0])
+            for i in range(self.NUMANG):
+                l.Angle_Coeffs[i][0] = self.TK[i]
+                l.Angle_Coeffs[i][1] = (180/math.pi) * self.TEQ[i]
+
+            l.Dihedral_Coeffs = []
+            for i in range(self.NPTRA):
+                l.Dihedral_Coeffs.append([0,0,0])
+            for i in range(self.NPTRA):
+                l.Dihedral_Coeffs[i][0] = self.PK[i]
+                if self.PHASE[i] == 0:
+                    l.Dihedral_Coeffs[i][1] = 1
+                else:
+                    l.Dihedral_Coeffs[i][1] = -1
+                l.Dihedral_Coeffs[i][2] = self.PN[i]
+
+            l.Atoms = []
+            for i in range(self.NATOM):
+                x = self.X[i]
+                y = self.Y[i]
+                z = self.Z[i]
+                if Shift:
+                    while x < l.xlo:
+                        x = x + self.BOX[0]
+                    while x > l.xhi:
+                        x = x - self.BOX[0]
+                    while y < l.ylo:
+                        y = y + self.BOX[1]
+                    while y > l.yhi:
+                        y = y - self.BOX[1]
+                    while z < l.zlo:
+                        z = z + self.BOX[2]
+                    while z > l.zhi:
+                        z = z - self.BOX[2]
+                l.Atoms.append([0, self.IAC[i], self.CHRG[i]/18.2223, \
+                                x, y, z])
+
+            l.Bonds = []
+            for i in range(l.bonds):
+                l.Bonds.append([0,0,0])
+            for i in range(self.NBONH):
+                l.Bonds[i][0] = self.ICBH[i]
+                l.Bonds[i][1] = abs(self.IBH[i])/3 + 1
+                l.Bonds[i][2] = abs(self.JBH[i])/3 + 1
+            for i in range(self.NBONA):
+                l.Bonds[self.NBONH + i][0] = self.ICB[i]
+                l.Bonds[self.NBONH + i][1] = abs(self.IB[i])/3 + 1
+                l.Bonds[self.NBONH + i][2] = abs(self.JB[i])/3 + 1
+
+            l.Angles = []
+            for i in range(l.angles):
+                l.Angles.append([0,0,0,0])
+            for i in range(self.NTHETH):
+                l.Angles[i][0] = self.ICTH[i]
+                l.Angles[i][1] = abs(self.ITH[i])/3 + 1
+                l.Angles[i][2] = abs(self.JTH[i])/3 + 1
+                l.Angles[i][3] = abs(self.KTH[i])/3 + 1
+            for i in range(self.NTHETA):
+                l.Angles[self.NTHETH + i][0] = self.ICT[i]
+                l.Angles[self.NTHETH + i][1] = abs(self.IT[i])/3 + 1
+                l.Angles[self.NTHETH + i][2] = abs(self.JT[i])/3 + 1
+                l.Angles[self.NTHETH + i][3] = abs(self.KT[i])/3 + 1
+
+            l.Dihedrals = []
+            for i in range(l.dihedrals):
+                l.Dihedrals.append([0,0,0,0,0])
+            for i in range(self.NPHIH):
+                l.Dihedrals[i][0] = self.ICPH[i]
+                l.Dihedrals[i][1] = abs(self.IPH[i])/3 + 1
+                l.Dihedrals[i][2] = abs(self.JPH[i])/3 + 1
+                l.Dihedrals[i][3] = abs(self.KPH[i])/3 + 1
+                l.Dihedrals[i][4] = abs(self.LPH[i])/3 + 1
+            for i in range(self.NPHIA):
+                l.Dihedrals[self.NPHIH + i][0] = self.ICP[i]
+                l.Dihedrals[self.NPHIH + i][1] = abs(self.IP[i])/3 + 1
+                l.Dihedrals[self.NPHIH + i][2] = abs(self.JP[i])/3 + 1
+                l.Dihedrals[self.NPHIH + i][3] = abs(self.KP[i])/3 + 1
+                l.Dihedrals[self.NPHIH + i][4] = abs(self.LP[i])/3 + 1
+
+            print 'done.'
+            return l
+        else:
+            print '(Error: Not all the Amber data has been read!)'
+    
+    #--------------------------------------------------------
+
+    def Read_data(self, Filename):
+        'Read the filename, returning a list of strings'
+
+        import string, sys
+
+        print 'Reading', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return
+
+        try:
+            Lines = F.readlines()
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+        F.close()
+
+        # If the first line is empty, use the Basename
+        if Filename[-4:] == '.crd':
+	    if string.split(Lines[0]) == []: # This line corresponds to TITLE name in CRD file
+                Basename = Filename[:string.find(Filename, '.')]
+                Item_list = [Basename]
+                print 'Warning: Title not present... Assigning Basename as Title'
+	    else:
+                Item_list = []
+	else:
+	    if string.split(Lines[3]) == []: # This line corresponds to TITLE name in TOPOLOGY file
+                Basename = Filename[:string.find(Filename, '.')]
+                Item_list = [Basename]
+                print 'Warning: Title not present... Assigning Basename as Title'
+            else:
+                Item_list = []
+
+        for Line in Lines:
+	    if Line[0]!='%': #Vikas' Modification: This condition ignores all the lines starting with % in the topology file.
+            	Item_list.extend(string.split(Line))
+
+        return Item_list
+
+    #--------------------------------------------------------
+
+    def Read_CRD(self, Basename):
+        'Read the Amber coordinate/restart (.crd) file'
+
+        # The optional velocities and periodic box size are not yet parsed.
+
+        Item_list = self.Read_data(Basename + '.crd')
+
+        if Item_list == None:
+            return
+        elif len(Item_list) < 2:
+            print '(error: File too short!)'
+            return
+
+        # Parse the data
+        if self.__dict__.has_key('ITITL'):
+            if Pop(Item_list,0) != self.ITITL:
+	        print '(warning: ITITL differs!)',
+        else:
+            self.ITITL = Pop(Item_list,0)
+        print self.ITITL #Vikas Modification : Priting the Title
+
+        if self.__dict__.has_key('NATOM'):
+            if eval(Pop(Item_list,0)) != self.NATOM:
+		print '(error: NATOM differs!)'
+                return
+        else:
+            self.NATOM = eval(Pop(Item_list,0))
+	print self.NATOM # Vikas' Modification: Printing number of atoms just to make sure that the program is reading the correct value. 
+
+        #if len(Item_list) == 1 + 3 * self.NATOM:
+        # Vikas' Modification: I changed the condition.
+	if (len(Item_list)%3) != 0:
+	    self.TIME = eval(Pop(Item_list,0))
+        else:
+            self.TIME = 0
+	print self.TIME # Vikas' Modification : Printing simulation time, just to make sure that the program is readint the correct value.
+        if len(Item_list) < 3 * self.NATOM:
+            print '(error: File too short!)'
+            return
+
+        self.X = []
+        self.Y = []
+        self.Z = []
+        for i in range(self.NATOM):
+            self.X.append(eval(Pop(Item_list,0)))
+            self.Y.append(eval(Pop(Item_list,0)))
+            self.Z.append(eval(Pop(Item_list,0)))
+
+        if (self.NATOM == 1) and len(Item_list):
+            print '(warning: Ambiguity!)',
+
+        if len(Item_list) >= 3 * self.NATOM:
+                self.VX = []
+                self.VY = []
+                self.VZ = []
+                for i in range(self.NATOM):
+                    self.VX.append(eval(Pop(Item_list,0)))
+                    self.VY.append(eval(Pop(Item_list,0)))
+                    self.VZ.append(eval(Pop(Item_list,0)))
+
+        if len(Item_list) >= 3:
+            self.BOX = []
+            for i in range(3):
+                self.BOX.append(eval(Pop(Item_list,0)))
+
+        if len(Item_list):
+            print '(warning: File too large!)',
+        
+        print 'done.'
+        self.CRD_is_read = 1
+
+    #--------------------------------------------------------
+
+    def Read_TOP(self, Basename):
+        'Read the Amber parameter/topology (.top) file'
+        Item_list = self.Read_data(Basename + '.top')
+
+        if Item_list == None:
+            return
+        elif len(Item_list) < 31:
+            print '(error: File too short!)'
+            return
+
+       # Parse the data
+        if self.__dict__.has_key('ITITL'):
+            if Pop(Item_list,0) != self.ITITL:
+                print '(warning: ITITL differs!)'
+        else:
+            self.ITITL = Pop(Item_list,0)
+	print self.ITITL # Printing Self Title
+
+        if self.__dict__.has_key('NATOM'):
+            if eval(Pop(Item_list,0)) != self.NATOM:
+                print '(error: NATOM differs!)'
+ 		return
+        else:
+            self.NATOM = eval(Pop(Item_list,0))
+        print self.NATOM # Printing total number of atoms just to make sure that thing are going right
+        self.NTYPES = eval(Pop(Item_list,0))
+        self.NBONH  = eval(Pop(Item_list,0))
+        self.MBONA  = eval(Pop(Item_list,0))
+        self.NTHETH = eval(Pop(Item_list,0))
+        self.MTHETA = eval(Pop(Item_list,0))
+        self.NPHIH  = eval(Pop(Item_list,0))
+        self.MPHIA  = eval(Pop(Item_list,0))
+        self.NHPARM = eval(Pop(Item_list,0))
+        self.NPARM  = eval(Pop(Item_list,0))
+        self.NEXT   = eval(Pop(Item_list,0))
+        self.NRES   = eval(Pop(Item_list,0))
+        self.NBONA  = eval(Pop(Item_list,0))
+        self.NTHETA = eval(Pop(Item_list,0))
+        self.NPHIA  = eval(Pop(Item_list,0))
+        self.NUMBND = eval(Pop(Item_list,0))
+        self.NUMANG = eval(Pop(Item_list,0))
+        self.NPTRA  = eval(Pop(Item_list,0))
+        self.NATYP  = eval(Pop(Item_list,0))
+        self.NPHB   = eval(Pop(Item_list,0))
+        self.IFPERT = eval(Pop(Item_list,0))
+        self.NBPER  = eval(Pop(Item_list,0))
+        self.NGPER  = eval(Pop(Item_list,0))
+        self.NDPER  = eval(Pop(Item_list,0))
+        self.MBPER  = eval(Pop(Item_list,0))
+        self.MGPER  = eval(Pop(Item_list,0))
+        self.MDPER  = eval(Pop(Item_list,0))
+        self.IFBOX  = eval(Pop(Item_list,0))
+        self.NMXRS  = eval(Pop(Item_list,0))
+        self.IFCAP  = eval(Pop(Item_list,0))
+
+        #....................................................
+
+        if len(Item_list) < 5 * self.NATOM + self.NTYPES**2 + \
+           2*(self.NRES + self.NUMBND + self.NUMANG) + \
+           3*self.NPTRA + self.NATYP:
+            print '(error: File too short!)'
+            return -1
+
+        self.IGRAPH = []
+        Pop(Item_list,0)
+
+	  # A little kludge is needed here, since the IGRAPH strings are
+        # not separated by spaces if 4 characters in length.
+        for i in range(self.NATOM):
+            if len(Item_list[0]) > 4:
+                Item_list.insert(1, Item_list[0][4:])
+                Item_list.insert(1, Item_list[0][0:4])
+                del Item_list[0]
+            self.IGRAPH.append(Pop(Item_list,0))
+        
+	# Vikas' Modification : In the following section, I am printing out each quantity which is currently being read from the topology file.
+	print 'Reading Charges...'
+        self.CHRG = []
+      	for i in range(self.NATOM):
+            self.CHRG.append(eval(Pop(Item_list,0)))
+
+        print 'Reading Atomic Masses...'
+	self.AMASS = []
+        for i in range(self.NATOM):
+            self.AMASS.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Atom Types...'
+        self.IAC = []
+        for i in range(self.NATOM):
+            self.IAC.append(eval(Pop(Item_list,0)))
+
+        print 'Reading Excluded Atoms...'
+	self.NUMEX = []
+        for i in range(self.NATOM):
+            self.NUMEX.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Non-bonded Parameter Index...'
+        self.ICO = []
+        for i in range(self.NTYPES**2):
+            self.ICO.append(eval(Pop(Item_list,0)))
+
+        print 'Reading Residue Labels...'
+	self.LABRES = []
+        for i in range(self.NRES):
+            self.LABRES.append(Pop(Item_list,0))
+
+        print 'Reading Residues Starting Pointers...'
+	self.IPRES = []
+        for i in range(self.NRES):
+            self.IPRES.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Bond Force Constants...'
+        self.RK = []
+        for i in range(self.NUMBND):
+            self.RK.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Equilibrium Bond Values...'
+        self.REQ = []
+        for i in range(self.NUMBND):
+            self.REQ.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Angle Force Constants...' 
+        self.TK = []
+        for i in range(self.NUMANG):
+            self.TK.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Equilibrium Angle Values...'
+        self.TEQ = []
+        for i in range(self.NUMANG):
+            self.TEQ.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Dihedral Force Constants...'
+        self.PK = []
+        for i in range(self.NPTRA):
+            self.PK.append(eval(Pop(Item_list,0)))
+        
+	print 'Reading Dihedral Periodicity...' 
+        self.PN = []
+        for i in range(self.NPTRA):
+            self.PN.append(eval(Pop(Item_list,0)))
+        
+	print 'Reading Dihedral Phase...'
+        self.PHASE = []
+        for i in range(self.NPTRA):
+            self.PHASE.append(eval(Pop(Item_list,0)))
+        
+	print 'Reading Solty...' #I think this is currently not used in AMBER. Check it out, though
+        self.SOLTY = []
+        for i in range(self.NATYP):
+            self.SOLTY.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if len(Item_list) < 2 * self.NTYPES * (self.NTYPES + 1) / 2:
+            print '(error: File too short!)'
+            return -1
+
+	print 'Reading LJ A Coefficient...'
+        self.CN1 = []
+        for i in range(self.NTYPES * (self.NTYPES + 1) / 2):
+            self.CN1.append(eval(Pop(Item_list,0)))
+
+	print 'Reading LJ B Coefficient...'
+        self.CN2 = []
+        for i in range(self.NTYPES * (self.NTYPES + 1) / 2):
+            self.CN2.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if len(Item_list) < 3 * (self.NBONH + self.NBONA) + \
+           4 * (self.NTHETH + self.NTHETA) + 5 * (self.NPHIH + self.NPHIA):
+            print '(error: File too short!)'
+            return -1
+
+	print 'Reading Bonds which include hydrogen...'
+        self.IBH = []
+        self.JBH = []
+        self.ICBH = []
+        for i in range(self.NBONH):
+            self.IBH.append(eval(Pop(Item_list,0)))
+            self.JBH.append(eval(Pop(Item_list,0)))
+            self.ICBH.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Bonds which dont include hydrogen...'
+        self.IB = []
+        self.JB = []
+        self.ICB = []
+        for i in range(self.NBONA):
+            self.IB.append(eval(Pop(Item_list,0)))
+            self.JB.append(eval(Pop(Item_list,0)))
+            self.ICB.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Angles which include hydrogen...' 
+        self.ITH = []
+        self.JTH = []
+        self.KTH = []
+        self.ICTH = []
+        for i in range(self.NTHETH):
+            self.ITH.append(eval(Pop(Item_list,0)))
+            self.JTH.append(eval(Pop(Item_list,0)))
+            self.KTH.append(eval(Pop(Item_list,0)))
+            self.ICTH.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Angles which dont include hydrogen...'
+        self.IT = []
+        self.JT = []
+        self.KT = []
+        self.ICT = []
+        for i in range(self.NTHETA):
+            self.IT.append(eval(Pop(Item_list,0)))
+            self.JT.append(eval(Pop(Item_list,0)))
+            self.KT.append(eval(Pop(Item_list,0)))
+            self.ICT.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Dihedrals which include hydrogen...'
+        self.IPH = []
+        self.JPH = []
+        self.KPH = []
+        self.LPH = []
+        self.ICPH = []
+        for i in range(self.NPHIH):
+            self.IPH.append(eval(Pop(Item_list,0)))
+            self.JPH.append(eval(Pop(Item_list,0)))
+            self.KPH.append(eval(Pop(Item_list,0)))
+            self.LPH.append(eval(Pop(Item_list,0)))
+            self.ICPH.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Dihedrals which dont include hydrogen...'
+        self.IP = []
+        self.JP = []
+        self.KP = []
+        self.LP = []
+        self.ICP = []
+        for i in range(self.NPHIA):
+            self.IP.append(eval(Pop(Item_list,0)))
+            self.JP.append(eval(Pop(Item_list,0)))
+            self.KP.append(eval(Pop(Item_list,0)))
+            self.LP.append(eval(Pop(Item_list,0)))
+            self.ICP.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if len(Item_list) < self.NEXT + 3 * self.NPHB + 4 * self.NATOM:
+            print '(error: File too short!)'
+            return -1
+
+	print 'Reading Excluded Atom List...'
+        self.NATEX = []
+        for i in range(self.NEXT):
+            self.NATEX.append(eval(Pop(Item_list,0)))
+
+	print 'Reading H-Bond A Coefficient, corresponding to r**12 term for all possible types...'
+        self.ASOL = []
+        for i in range(self.NPHB):
+            self.ASOL.append(eval(Pop(Item_list,0)))
+
+	print 'Reading H-Bond B Coefficient, corresponding to r**10 term for all possible types...'
+        self.BSOL = []
+        for i in range(self.NPHB):
+            self.BSOL.append(eval(Pop(Item_list,0)))
+
+	print 'Reading H-Bond Cut...' # I think it is not being used nowadays
+        self.HBCUT = []
+        for i in range(self.NPHB):
+            self.HBCUT.append(eval(Pop(Item_list,0)))
+
+	print 'Reading Amber Atom Types for each atom...'
+        self.ISYMBL = []
+        for i in range(self.NATOM):
+            self.ISYMBL.append(Pop(Item_list,0))
+
+	print 'Reading Tree Chain Classification...'
+        self.ITREE = []
+        for i in range(self.NATOM):
+            self.ITREE.append(Pop(Item_list,0))
+
+	print 'Reading Join Array: Tree joining information' # Currently unused in Sander, an AMBER module
+        self.JOIN = []
+        for i in range(self.NATOM):
+            self.JOIN.append(eval(Pop(Item_list,0)))
+
+	print 'Reading IRotate...' # Currently unused in Sander and Gibbs
+        self.IROTAT = []
+        for i in range(self.NATOM):
+            self.IROTAT.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if self.IFBOX > 0:
+            if len(Item_list) < 3:
+                print '(error: File too short!)'
+                return -1
+
+            print 'Reading final residue which is part of solute...'
+	    self.IPTRES = eval(Pop(Item_list,0))
+	    print 'Reading total number of molecules...'
+            self.NSPM = eval(Pop(Item_list,0))
+	    print 'Reading first solvent moleule index...'
+            self.NSPSOL = eval(Pop(Item_list,0))
+
+            if len(Item_list) < self.NSPM + 4:
+                print '(error: File too short!)'
+                return -1
+
+	    print 'Reading atom per molecule...' 
+            self.NSP = []
+            for i in range(self.NSPM):
+                self.NSP.append(eval(Pop(Item_list,0)))
+
+            self.BETA = eval(Pop(Item_list,0))
+
+	    print 'Reading Box Dimensions...' 
+            if self.__dict__.has_key('BOX'):
+                BOX = []
+                for i in range(3):
+                    BOX.append(eval(Pop(Item_list,0)))
+                for i in range(3):
+                    if BOX[i] != self.BOX[i]:
+                        print '(warning: BOX differs!)',
+                        break
+                del BOX
+            else:
+                self.BOX = []
+                for i in range(3):
+                    self.BOX.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if self.IFCAP > 0:
+            if len(Item_list) < 5:
+                print '(error: File too short!)'
+                return -1
+	    print 'Reading ICAP variables::: For details, refer to online AMBER format manual'
+            self.NATCAP = eval(Pop(Item_list,0))
+            self.CUTCAP = eval(Pop(Item_list,0))
+            self.XCAP = eval(Pop(Item_list,0))
+            self.YCAP = eval(Pop(Item_list,0))
+            self.ZCAP = eval(Pop(Item_list,0))
+
+        #....................................................
+
+        if self.IFPERT > 0:
+            if len(Item_list) < 4 * self.NBPER + 5 * self.NGPER + \
+               6 * self.NDPER + self.NRES + 6 * self.NATOM:
+                print '(error: File too short!)'
+                return -1
+
+	    print 'Reading perturb variables, 1. Bond, 2. Angles, 3. Dihedrals, etc etc.::: For details, refer to online AMBER format manual' 
+            self.IBPER = []
+            self.JBPER = []
+            for i in range(self.NBPER):
+                self.IBPER.append(eval(Pop(Item_list,0)))
+                self.JBPER.append(eval(Pop(Item_list,0)))
+
+            self.ICBPER = []
+            for i in range(2 * self.NBPER):
+                self.ICBPER.append(eval(Pop(Item_list,0)))
+
+            self.ITPER = []
+            self.JTPER = []
+            self.KTPER = []
+            for i in range(self.NGPER):
+                self.ITPER.append(eval(Pop(Item_list,0)))
+                self.JTPER.append(eval(Pop(Item_list,0)))
+                self.KTPER.append(eval(Pop(Item_list,0)))
+
+            self.ICTPER = []
+            for i in range(2 * self.NGPER):
+                self.ICTPER.append(eval(Pop(Item_list,0)))
+
+            self.IPPER = []
+            self.JPPER = []
+            self.KPPER = []
+            self.LPPER = []
+            for i in range(self.NDPER):
+                self.IPPER.append(eval(Pop(Item_list,0)))
+                self.JPPER.append(eval(Pop(Item_list,0)))
+                self.KPPER.append(eval(Pop(Item_list,0)))
+                self.LPPER.append(eval(Pop(Item_list,0)))
+
+            self.ICPPER = []
+            for i in range(2 * self.NDPER):
+                self.ICPPER.append(eval(Pop(Item_list,0)))
+
+            LABRES = []
+            for i in range(self.NRES):
+                LABRES.append(Pop(Item_list,0))
+            for i in range(self.NRES):
+                if LABRES[i] != self.LABRES[i]:
+                    print '(warning: BOX differs!)',
+                    break
+
+            self.IGRPER = []
+            for i in range(self.NATOM):
+                self.IGRPER.append(eval(Pop(Item_list,0)))
+
+            self.ISMPER = []
+            for i in range(self.NATOM):
+                self.ISMPER.append(eval(Pop(Item_list,0)))
+
+            self.ALMPER = []
+            for i in range(self.NATOM):
+                self.ALMPER.append(eval(Pop(Item_list,0)))
+
+            self.IAPER = []
+            for i in range(self.NATOM):
+                self.IAPER.append(eval(Pop(Item_list,0)))
+
+            self.IACPER = []
+            for i in range(self.NATOM):
+                self.IACPER.append(eval(Pop(Item_list,0)))
+
+            self.CGPER = []
+            for i in range(self.NATOM):
+                self.CGPER.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        self.IPOL = 0
+        if self.IPOL == 1:
+            if len(Item_list) < self.NATOM:
+                print '(error: File too short!)'
+                return -1
+	    print 'Reading Polarizability Data. For details, refer to online AMBER format manual'
+            self.ATPOL = []
+            for i in range(self.NATOM):
+                self.ATPOL.append(eval(Pop(Item_list,0)))
+
+            if self.IFPERT == 1:
+                if len(Item_list) < self.NATOM:
+                    print '(error: File too short!)'
+                    return -1
+                self.ATPOL1 = []
+                for i in range(self.NATOM):
+                    self.ATPOL1.append(eval(Pop(Item_list,0)))
+
+        #....................................................
+
+        if len(Item_list):
+            print '(warning: File too large!)',
+
+        print 'done.'
+        self.TOP_is_read = 1
+
+#============================================================
+
+def Find_Amber_files():
+    'Look for sets of Amber files to process'
+    '''If not passed anything on the command line, look for pairs of
+    Amber files (.crd and .top) in the current directory.  For
+    each set if there is no corresponding Lammps file (data.), or it is
+    older than any of the Amber files, add its basename to a list of
+    strings.  This list is returned by the function'''
+
+    # Date and existence checks not yet implemented
+
+    import os, sys
+
+    Basename_list = []
+
+    # Extract basenames from command line
+    for Name in sys.argv[1:]:
+        if Name[-4:] == '.crd':
+            Basename_list.append(Name[:-4])
+        else:
+            if Name[-4:] == '.top':
+                Basename_list.append(Name[:-4])
+            else:
+                Basename_list.append(Name)
+
+    # Remove duplicate basenames
+    for Basename in Basename_list[:]:
+        while Basename_list.count(Basename) > 1:
+            Basename_list.remove(Basename)
+
+    if Basename_list == []:
+        print 'Looking for Amber files...',
+        Dir_list = os.listdir('.')
+        Dir_list.sort()
+        for File in Dir_list:
+            if File[-4:] == '.top':
+                Basename = File[:-4]
+                if (Basename + '.crd') in Dir_list:
+                    Basename_list.append(Basename)
+        if Basename_list != []:
+            print 'found',
+            for i in range(len(Basename_list)-1):
+                print Basename_list[i] + ',',
+            print Basename_list[-1] + '\n'
+    
+    if Basename_list == []:
+        print 'none.\n'
+
+    return Basename_list
+    
+#============================================================
+
+def Convert_Amber_files():
+    'Handle the whole conversion process'
+    print
+    print 'Welcome to amber2lammps, a program to convert Amber files to Lammps format!'
+    print
+    Basename_list = Find_Amber_files()
+    for Basename in Basename_list:
+        a = Amber()
+        a.Read_CRD(Basename)
+        if a.CRD_is_read:
+            a.Read_TOP(Basename)
+            if a.TOP_is_read:
+                l = a.Coerce_to_Lammps()
+                l.Write_Lammps(Basename)
+                del l
+        del a
+        print
+
+#============================================================
+
+Convert_Amber_files()

tools/amber2lmp/dump2trj.py

@@ -0,0 +1,306 @@
+#! /usr/freeware/bin/python
+
+#
+# This is dump2trj, a program written by Keir E. Novik to convert
+# Lammps position dump files to Amber trajectory files.
+#
+# Copyright 2000, 2001 Keir E. Novik; all rights reserved.
+# 
+# Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README
+#
+
+#============================================================
+
+def Convert_files():
+    'Handle the whole conversion process'
+
+    print
+    print 'Welcome to dump2trj, a program to convert Lammps position dump files to\nAmber trajectory format!'
+    print
+
+    Basename_list = Find_dump_files()
+
+    for Basename in Basename_list:
+        t = Trajectory()
+        if t.Read_dump(Basename):
+            t.Write_trj(Basename)
+        del t
+        print
+
+#============================================================
+
+def Find_dump_files():
+    'Look for sets of Lammps position dump files to process'
+
+    '''If passed something on the command line, treat it as a list of
+    files to process.  Otherwise, look for *.dump in the current
+    directory.
+    '''
+
+    import os, sys
+
+    Basename_list = []
+
+    # Extract basenames from command line
+    for Name in sys.argv[1:]:
+        if Name[-5:] == '.dump':
+            Basename_list.append(Name[:-5])
+        else:
+            Basename_list.append(Name)
+
+    if Basename_list == []:
+        print 'Looking for Lammps dump files...',
+        Dir_list = os.listdir('.')
+        for Filename in Dir_list:
+            if Filename[-5:] == '.dump':
+                Basename_list.append(Filename[:-5])
+        Basename_list.sort()
+        if Basename_list != []:
+            print 'found',
+            for i in range(len(Basename_list)-1):
+                print Basename_list[i] + ',',
+            print Basename_list[-1] + '\n'
+    
+    if Basename_list == []:
+        print 'none.\n'
+
+    return Basename_list
+    
+#============================================================
+
+class Snapshot:
+    def __init__(self, The_trajectory):
+        'Initialise the Snapshot class'
+        
+        self.timestep = The_trajectory.timestep
+        self.atoms = The_trajectory.atoms
+        self.xlo = The_trajectory.xlo
+        self.xhi = The_trajectory.xhi
+        self.ylo = The_trajectory.ylo
+        self.yhi = The_trajectory.yhi
+        self.zlo = The_trajectory.zlo
+        self.zhi = The_trajectory.zhi
+
+    #--------------------------------------------------------
+
+    def Read_dump(self, Lines):
+        'Read a snapshot (timestep) from a Lammps position dump file'
+
+        '''Trajectory.Read_dump() will pass us only the lines we need.
+        '''
+
+        self.Atom_list = Lines
+        
+    #--------------------------------------------------------
+
+    def Write_trj(self, F):
+        'Write a snapshot (timestep) to an Amber trajectory file'
+
+        '''The Atom_list must be sorted, as it may not be in order
+        (for example, in a parallel Lammps simulation).
+        '''
+
+        import string
+
+        xBOX = (self.xhi - self.xlo)
+        yBOX = (self.yhi - self.ylo)
+        zBOX = (self.zhi - self.zlo)
+
+        Min = min(self.xlo, self.ylo, self.zlo)
+        Max = max(self.xhi, self.yhi, self.zhi, xBOX, yBOX, zBOX)
+        if Min <= -1000 or Max >= 10000:
+            print '(error: coordinates too large!)'
+            return
+
+        Print_list = []
+
+        for Line in NumericalSort(self.Atom_list):
+            Item_list = string.split(Line)
+            x = xBOX * (Float(Item_list[2])+Float(Item_list[5])) # Modified main box x-coordinate to actual x-coordinate
+            y = yBOX * (Float(Item_list[3])+Float(Item_list[6])) # Modified main box y-coordinate to actual y-coordinate 
+            z = zBOX * (Float(Item_list[4])+Float(Item_list[7])) # Modified main box z-coordinate to actual z-coordinate
+            Print_list.append('%(x)8.3f' % vars())
+            Print_list.append('%(y)8.3f' % vars())
+            Print_list.append('%(z)8.3f' % vars())
+
+            if len(Print_list) > 9:
+                Line = ''
+                for j in range(10):
+                    Line = Line + Print_list[j]
+                Line = Line + '\n'
+                Print_list = Print_list[10:]
+
+                try:
+                    F.write(Line)
+                except IOError, Detail:
+                    print '(error:', Detail[1] + '!)'
+                    F.close()
+                    return
+
+        if len(Print_list) > 0:
+            Line = ''
+            for j in range(len(Print_list)):
+                Line = Line + Print_list[j]
+            Line = Line + '\n'
+
+            try:
+                F.write(Line)
+            except IOError, Detail:
+                print '(error:', Detail[1] + '!)'
+                F.close()
+                return
+                
+        Line = '%(xBOX)8.3f%(yBOX)8.3f%(zBOX)8.3f\n' % vars()
+        try:
+            F.write(Line)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+#============================================================
+
+class Trajectory:
+
+    def Read_dump(self, Basename):
+        'Read a Lammps position dump file'
+
+        import string, sys
+
+        Filename = Basename + '.dump'
+
+        print 'Reading', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return 0
+
+        try:
+            Lines = F.readlines()
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return 0
+
+        F.close()
+
+        i = 0
+        self.Snapshot_list = []
+
+        # Parse the dump
+        while i < len(Lines):
+
+            if string.find(Lines[i], 'ITEM: TIMESTEP') != -1:
+                # Read the timestep
+                self.timestep = int(Lines[i+1])
+                i = i + 2
+
+            elif string.find(Lines[i], 'ITEM: NUMBER OF ATOMS') != -1:
+                # Read the number of atoms
+                self.atoms = int(Lines[i+1])
+                i = i + 2
+
+            elif string.find(Lines[i], 'ITEM: BOX BOUNDS') != -1:
+                # Read the periodic box boundaries
+                Item_list = string.split(Lines[i+1])
+                self.xlo = Float(Item_list[0])
+                self.xhi = Float(Item_list[1])
+                Item_list = string.split(Lines[i+2])
+                self.ylo = Float(Item_list[0])
+                self.yhi = Float(Item_list[1])
+                Item_list = string.split(Lines[i+3])
+                self.zlo = Float(Item_list[0])
+                self.zhi = Float(Item_list[1])
+                i = i + 4
+
+            elif string.find(Lines[i], 'ITEM: ATOMS') != -1:
+                # Read atom positions
+                self.Snapshot_list.append(Snapshot(self))
+                Start = i + 1
+                End = Start + self.atoms
+                self.Snapshot_list[-1].Read_dump(Lines[Start:End])
+                i = i + self.atoms + 1
+                
+            else:
+                print '(error: unknown line in file!)'
+                return
+
+        print 'done.'
+        return 1
+
+    #--------------------------------------------------------
+
+    def Write_trj(self, Basename):
+        'Write an Amber trajectory file'
+
+        import os, sys
+
+        Filename = Basename + '.mdcrd'
+
+        Dir_list = os.listdir('.')
+        i = 1
+        while Filename in Dir_list:
+            Filename = Basename + `i` + '.mdcrd'
+            i = i + 1
+        del i
+
+        print 'Writing', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename, 'w')
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return
+
+        try:
+            F.write(Basename + '\n')
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+        for S in self.Snapshot_list:
+            S.Write_trj(F)
+
+        F.close()
+        print 'done.'
+
+#============================================================
+
+def Float(s):
+    'Return the string s as a float, if possible'
+
+    try:
+        x = float(s)
+    except ValueError:
+        if s[-1] == ',':
+            s = s[:-1]
+        x = float(s)
+
+    return x
+
+#============================================================
+
+def NumericalSort(String_list):
+    'Sort a list of strings by the integer value of the first element'
+
+    import string
+
+    Working_list = []
+    for s in String_list:
+        Working_list.append((int(string.split(s)[0]), s))
+
+    Working_list.sort()
+
+    Return_list = []
+    for Tuple in Working_list:
+        Return_list.append(Tuple[1])
+    return Return_list
+
+#============================================================
+
+Convert_files()

tools/amber2lmp/dump2trj99.py

@@ -0,0 +1,277 @@
+#! /usr/freeware/bin/python
+
+#
+# This is dump2trj, a program written by Keir E. Novik to convert
+# Lammps position dump files to Amber trajectory files.
+#
+# Copyright 2000 Keir E. Novik; all rights reserved.
+# 
+
+#============================================================
+
+def Convert_files():
+    'Handle the whole conversion process'
+
+    print
+    print 'Welcome to dump2trj, a program to convert Lammps position dump files to\nAmber trajectory format!'
+    print
+
+    Basename_list = Find_dump_files()
+
+    for Basename in Basename_list:
+        t = Trajectory()
+        if t.Read_dump(Basename):
+            t.Write_trj(Basename)
+        del t
+        print
+
+#============================================================
+
+def Find_dump_files():
+    'Look for sets of Lammps position dump files to process'
+
+    '''If passed something on the command line, treat it as a list of
+    files to process.  Otherwise, look for *.dump in the current
+    directory.
+    '''
+
+    import os, sys
+
+    Basename_list = []
+
+    # Extract basenames from command line
+    for Name in sys.argv[1:]:
+        if Name[-5:] == '.dump':
+            Basename_list.append(Name[:-5])
+        else:
+            Basename_list.append(Name)
+
+    if Basename_list == []:
+        print 'Looking for Lammps dump files...',
+        Dir_list = os.listdir('.')
+        for Filename in Dir_list:
+            if Filename[-5:] == '.dump':
+                Basename_list.append(Filename[:-5])
+        Basename_list.sort()
+        if Basename_list != []:
+            print 'found',
+            for i in range(len(Basename_list)-1):
+                print Basename_list[i] + ',',
+            print Basename_list[-1] + '\n'
+    
+    if Basename_list == []:
+        print 'none.\n'
+
+    return Basename_list
+    
+#============================================================
+
+class Snapshot:
+    def __init__(self, The_trajectory):
+        'Initialise the Snapshot class'
+        
+        self.atoms = The_trajectory.atoms
+        self.xlo = The_trajectory.xlo
+        self.xhi = The_trajectory.xhi
+        self.ylo = The_trajectory.ylo
+        self.yhi = The_trajectory.yhi
+        self.zlo = The_trajectory.zlo
+        self.zhi = The_trajectory.zhi
+
+    #--------------------------------------------------------
+
+    def Read_dump(self, Lines):
+        'Read a snapshot (timestep) from a Lammps position dump file'
+
+        '''Trajectory.Read_dump() will pass us only the lines we need
+        (including the timestep number).
+        '''
+
+        self.Atom_list = Lines[3:]
+        
+    #--------------------------------------------------------
+
+    def Write_trj(self, F):
+        'Write a snapshot (timestep) to an Amber trajectory file'
+
+        '''The Atom_list must be sorted, as it may not be in order
+        (for example, in a parallel Lammps simulation).  The first
+        element (before the sort) is the header line.
+        '''
+
+        import string
+
+        xBOX = (self.xhi - self.xlo)
+        yBOX = (self.yhi - self.ylo)
+        zBOX = (self.zhi - self.zlo)
+
+        Min = min(self.xlo, self.ylo, self.zlo)
+        Max = max(self.xhi, self.yhi, self.zhi, xBOX, yBOX, zBOX)
+        if Min <= -1000 or Max >= 10000:
+            print '(error: coordinates too large!)'
+            return
+
+        Print_list = []
+
+        self.Atom_list = self.Atom_list[1:]
+        self.Atom_list.sort()
+
+        for Line in self.Atom_list:
+            Item_list = string.split(Line)
+            x = xBOX * Float(Item_list[2])
+            y = yBOX * Float(Item_list[3])
+            z = zBOX * Float(Item_list[4])
+            Print_list.append('%(x)8.3f' % vars())
+            Print_list.append('%(y)8.3f' % vars())
+            Print_list.append('%(z)8.3f' % vars())
+
+            if len(Print_list) > 9:
+                Line = ''
+                for j in range(10):
+                    Line = Line + Print_list[j]
+                Line = Line + '\n'
+                Print_list = Print_list[10:]
+
+                try:
+                    F.write(Line)
+                except IOError, Detail:
+                    print '(error:', Detail[1] + '!)'
+                    F.close()
+                    return
+
+        if len(Print_list) > 0:
+            Line = ''
+            for j in range(len(Print_list)):
+                Line = Line + Print_list[j]
+            Line = Line + '\n'
+
+            try:
+                F.write(Line)
+            except IOError, Detail:
+                print '(error:', Detail[1] + '!)'
+                F.close()
+                return
+                
+        Line = '%(xBOX)8.3f%(yBOX)8.3f%(zBOX)8.3f\n' % vars()
+        try:
+            F.write(Line)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+#============================================================
+
+class Trajectory:
+    #--------------------------------------------------------
+
+    def Read_dump(self, Basename):
+        'Read a Lammps position dump file'
+
+        import string, sys
+
+        Filename = Basename + '.dump'
+
+        print 'Reading', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename)
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return 0
+
+        try:
+            Lines = F.readlines()
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return 0
+
+        F.close()
+
+        # Read the number of atoms
+        self.atoms = int(Lines[1])            
+
+        # Read the periodic box boundaries
+        Item_list = string.split(Lines[3])
+        self.xlo = Float(Item_list[0])
+        self.xhi = Float(Item_list[1])
+        Item_list = string.split(Lines[4])
+        self.ylo = Float(Item_list[0])
+        self.yhi = Float(Item_list[1])
+        Item_list = string.split(Lines[5])
+        self.zlo = Float(Item_list[0])
+        self.zhi = Float(Item_list[1])
+
+        # Read atom positions in each snapshot
+        Snapshots = (len(Lines) - 6) / (self.atoms + 3)
+        if int(Snapshots) != Snapshots:
+            print '(error: wrong length of dump!)'
+            return
+
+        self.Snapshot_list = []
+        for i in range(Snapshots):
+            self.Snapshot_list.append(Snapshot(self))
+            Start = 5 + i * (self.atoms + 3)
+            End = Start + (self.atoms + 3) + 1
+            self.Snapshot_list[-1].Read_dump(Lines[Start:End])
+
+        print 'done.'
+        return 1
+
+    #--------------------------------------------------------
+
+    def Write_trj(self, Basename):
+        'Write an Amber trajectory file'
+
+        import os, sys
+
+        Filename = Basename + '.x'
+
+        Dir_list = os.listdir('.')
+        i = 1
+        while Filename in Dir_list:
+            Filename = Basename + `i` + '.x'
+            i = i + 1
+        del i
+
+        print 'Writing', Filename + '...',
+        sys.stdout.flush()
+
+        try:
+            F = open(Filename, 'w')
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            return
+
+        try:
+            F.write(Basename + '\n')
+        except IOError, Detail:
+            print '(error:', Detail[1] + '!)'
+            F.close()
+            return
+
+        for S in self.Snapshot_list:
+            S.Write_trj(F)
+
+        F.close()
+        print 'done.'
+
+#============================================================
+
+def Float(s):
+    'Return the string s as a float, if possible'
+
+    try:
+        x = float(s)
+    except ValueError:
+        if s[-1] == ',':
+            s = s[:-1]
+        x = float(s)
+
+    return x
+
+#============================================================
+
+Convert_files()

tools/binary2txt.cpp

@@ -0,0 +1,122 @@
+/* -----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   www.cs.sandia.gov/~sjplimp/lammps.html
+   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------ */
+
+// Convert one or more LAMMPS binary dump files to ASCII text files
+//
+// this serial code must be compiled on a platform that can read the binary
+//   dump files since binary formats are not compatible across all platforms
+//
+// Syntax: binary2txt file1 file2 ...
+// Creates:           file1.txt file2.txt ...
+
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+
+main(int narg, char **arg)
+{
+  int i,j,k,m,n;
+  int ntimestep,natoms,size_one,nchunk;
+  double xlo,xhi,ylo,yhi,zlo,zhi;
+  int maxbuf = 0;
+  double *buf = NULL;
+
+  if (narg == 1) {
+    printf("Syntax: binary2txt file1 file2 ...\n");
+    exit(1);
+  }
+
+  // loop over files
+
+  for (int iarg = 1; iarg < narg; iarg++) {
+    printf("%s:",arg[iarg]);
+    fflush(stdout);
+    FILE *fp = fopen(arg[iarg],"rb");
+    if (!fp) {
+      printf("ERROR: Could not open %s\n",arg[iarg]);
+      exit(1);
+    }
+
+    n = strlen(arg[iarg]) + 1 + 4;
+    char *filetxt = new char[n];
+    strcpy(filetxt,arg[iarg]);
+    strcat(filetxt,".txt");
+    FILE *fptxt = fopen(filetxt,"w");
+    delete [] filetxt;
+
+    // loop over snapshots in file
+
+    while (1) {
+
+      fread(&ntimestep,sizeof(int),1,fp);
+
+      // detect end-of-file
+
+      if (feof(fp)) {
+	fclose(fp);
+	fclose(fptxt);
+	break;
+      }
+
+      fread(&natoms,sizeof(int),1,fp);
+      fread(&xlo,sizeof(double),1,fp);
+      fread(&xhi,sizeof(double),1,fp);
+      fread(&ylo,sizeof(double),1,fp);
+      fread(&yhi,sizeof(double),1,fp);
+      fread(&zlo,sizeof(double),1,fp);
+      fread(&zhi,sizeof(double),1,fp);
+      fread(&size_one,sizeof(int),1,fp);
+      fread(&nchunk,sizeof(int),1,fp);
+      
+      fprintf(fptxt,"ITEM: TIMESTEP\n");
+      fprintf(fptxt,"%d\n",ntimestep);
+      fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
+      fprintf(fptxt,"%d\n",natoms);
+      fprintf(fptxt,"ITEM: BOX BOUNDS\n");
+      fprintf(fptxt,"%g %g\n",xlo,xhi);
+      fprintf(fptxt,"%g %g\n",ylo,yhi);
+      fprintf(fptxt,"%g %g\n",zlo,zhi);
+      fprintf(fptxt,"ITEM: ATOMS\n");
+
+      // loop over processor chunks in file
+
+      for (i = 0; i < nchunk; i++) {
+	fread(&n,sizeof(int),1,fp);
+
+	// extend buffer to fit chunk size
+	
+	if (n > maxbuf) {
+	  if (buf) delete [] buf;
+	  buf = new double[n];
+	  maxbuf = n;
+	}
+
+	// read chunk and write as size_one values per line
+
+	fread(buf,sizeof(double),n,fp);
+	n /= size_one;
+	m = 0;
+	for (j = 0; j < n; j++) {
+	  for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
+	  fprintf(fptxt,"\n");
+	}
+      }
+
+      printf(" %d",ntimestep);
+      fflush(stdout);
+    }
+    printf("\n");
+  }
+
+  if (buf) delete [] buf;
+}

tools/ch2lmp/README

@@ -0,0 +1,130 @@
+These tools were created by Pieter J. in 't Veld (pjintve@sandia.gov)
+and Paul Crozier (pscrozi@sandia.gov), Sandia National Laboratories,
+2005. They are intended to make it easy to use CHARMM as a builder and
+as a post-processor for LAMMPS. Using charmm2lammps.pl, you can
+convert an ensemble built in CHARMM into its LAMMPS equivalent.  Using
+lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
+
+In this directory, you should find:
+1) A perl script called "charmm2lammps.pl"
+2) A perl script called "lammps2pdb.pl"
+3) An "example" folder containing an example of how to use these tools.
+4) An "other" folder containing other potentially useful tools.
+
+In addition, you will need to provide the following input for 
+charmm2lammps.pl:
+1) a CHARMM parameter file (par_<forcefield>.prm)
+2) a CHARMM topology file (top_<forcefield>.rtf)
+3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb)
+4) a CHARMM psf file (<project>.psf)
+
+To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
+[-option[=#]] <forcefield> <project>" where <forcefield> is the name
+of the CHARMM FF you are using, (i.e. all22_prot), and <project> is
+the common name of your *.crd and *.psf files. The options for the
+script are listed below. If the option requires a parameter, the
+syntax must be [-option[=#]], (i.e. -border=5).
+
+-help        "display available options",                                    
+-charmm      "add charmm types to LAMMPS data file",                    
+-water       "add TIP3P water [default: 1 g/cc]",                       
+-ions        "add (counter)ions using Na+ and Cl- [default: 0 mol/l]",  
+-center      "recenter atoms",                                          
+-quiet       "do not print info",                                       
+-pdb_ctrl    "output project_ctrl.pdb",                                 
+-l           "set x-, y-, and z-dimensions simultaneously",             
+-lx          "x-dimension of simulation box",                           
+-ly          "y-dimension of simulation box",                           
+-lz          "z-dimension of simulation box",                           
+-border      "add border to all sides of simulation box [default: 0 A]",
+-ax          "rotation around x-axis",                                  
+-ay          "rotation around y-axis",                                  
+-az          "rotation around z-axis"                                   
+
+In the "example" folder, you will find example files that were created
+by following the steps below. These steps describe how to take a
+biomolecule and convert it into LAMMPS input, and then create a *.pdb
+trajectory from the LAMMPS output.
+
+1) Get the pdb file you want to model. http://www.rcsb.org/pdb/ For
+this example, we will use 1ac7.pdb
+
+2) If there are multiple models in the pdb file, choose the one you
+want and delete the others. Save the pared-down file as 1ac7_pared.pdb
+
+3) Download the charmm FF files and choose the one you want from the
+tarball.  We will use all27_na for this example.
+http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
+toppar_c31b1.tar.gz
+
+4) Create a *.pgn file for use with psfgen (you will need to have VMD
+installed, http://www.ks.uiuc.edu/Research/vmd/ ). This is the hardest
+step because you have to change the residue names from what the *.pdb
+file has to the corresponding names in the charmm FF files. You'll
+need to add a "pdbalias residue x xnew" line for each change that
+needs to be made.  The *.pgn should contain something like this:
+
+package require psfgen   
+topology top_all27_na.rtf
+pdbalias residue A ADE 
+pdbalias residue T THY 
+pdbalias residue G GUA 
+pdbalias residue C CYT 
+.
+.
+.
+segment A {pdb 1ac7_pared.pdb}   
+coordpdb 1ac7_pared.pdb A   
+guesscoord   
+writepdb 1ac7.pdb   
+writepsf charmm 1ac7.psf  
+exit 
+
+5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
+   1ac7.pdb file.
+
+6) Run charmm2lammps.pl by typing: 
+"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"
+
+7) Run lammps by typing: "lmp < 1ac7.in"
+
+8) Run lammps2pdb.pl by typing: "perl lammps2pdb.pl 1ac7"
+
+** Additional notes:
+
+The charmm2lammps.pl script takes the pdb and psf files for the 1ac7
+molecule and converts them into LAMMPS format. The -water option
+embeds the molecule in water on a crystal lattice. The -border option
+includes a layer of water surrounding the minimum dimensions of the
+molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
+can be visualized in a standard visualization package such as VMD. The
+-charmm option put comments into the LAMMPS data file (everything
+after the # sign is a comment) for user convenience in tracking atom
+types etc. according to CHARMM nomenclature.
+
+The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
+can typically be increased to 2 fs after equilibration if the bonds
+involving H are constrained via shake. Also, after equilibration, the
+delay on neigh_modify can probably increased to 5 or so to improve
+speed.
+
+The -ions option allows the user to neutralize the simulation cell
+with Na+ or Cl- counterions if the molecule has a net
+charge. Additional salt can be added by increasing the default
+concentration (i.e. -ions=0.5).
+
+** In the "other" file folder, you will find:
+
+1) A FORTRAN 90 code called "mkpdb.f". Requires "in_mkpdb".  This is a
+   fortran code that is an alternative way to convert LAMMPS dump
+   files into pdb format.
+
+2) A FORTRAN 90 code called "mkdcd.f" (and a FORTRAN 77 version called
+   mkdcd_f77.f).  Requires "in_mkdcd". Creates CHARMM format
+   trajectories from LAMMPS dump files.
+
+3) A 3rd party perl script called "crd2pdb.pl"
+
+4) A 3rd party fortran code called "pdb_to_crd.f"
+
+

tools/ch2lmp/example/1ac7.in

@@ -0,0 +1,31 @@
+# Created by charmm2lammps v1.6.2 on Fri Jun  3 14:07:02 MDT 2005
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       1ac7.data
+
+special_bonds   charmm
+fix             1 all nve
+fix             2 all shake 1e-6 500 0 m 1.0 a 93
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1
+thermo_style    multi
+timestep        0.5
+
+restart         10 1ac7.restart1 1ac7.restart2
+dump            1 all atom 10 1ac7.dump
+dump_modify     1 image yes scale yes
+
+run             20

tools/ch2lmp/example/1ac7.pdb

@@ -0,0 +1,529 @@
+REMARK original generated coordinate pdb file
+ATOM      1  P   ADE     1       3.759   0.457   0.076  0.00  0.00      A   
+ATOM      2  O1P ADE     1       2.779   0.279   0.171  0.00  0.00      A   
+ATOM      3  O2P ADE     1       4.489  -0.205   0.246  0.00  0.00      A   
+ATOM      4  O5' ADE     1       3.969   1.972  -0.393  1.00  0.00      A   
+ATOM      5  C5' ADE     1       5.044   2.279  -1.290  1.00  0.00      A   
+ATOM      6  H5' ADE     1       4.671   2.290  -2.305  1.00  0.00      A   
+ATOM      7 H5'' ADE     1       5.816   1.501  -1.189  1.00  0.00      A   
+ATOM      8  C4' ADE     1       5.648   3.651  -1.028  1.00  0.00      A   
+ATOM      9  H4' ADE     1       6.646   3.694  -1.462  1.00  0.00      A   
+ATOM     10  O4' ADE     1       4.831   4.694  -1.619  1.00  0.00      A   
+ATOM     11  C1' ADE     1       4.388   5.605  -0.589  1.00  0.00      A   
+ATOM     12  H1' ADE     1       4.979   6.519  -0.638  1.00  0.00      A   
+ATOM     13  N9  ADE     1       2.960   5.940  -0.745  1.00  0.00      A   
+ATOM     14  C5  ADE     1       1.063   7.037  -0.974  1.00  0.00      A   
+ATOM     15  N7  ADE     1       0.730   5.679  -1.026  1.00  0.00      A   
+ATOM     16  C8  ADE     1       1.887   5.123  -0.884  1.00  0.00      A   
+ATOM     17  H8  ADE     1       1.997   4.038  -0.875  1.00  0.00      A   
+ATOM     18  N1  ADE     1       0.950   9.380  -0.971  1.00  0.00      A   
+ATOM     19  C2  ADE     1       2.273   9.407  -0.803  1.00  0.00      A   
+ATOM     20  H2  ADE     1       2.731  10.392  -0.730  1.00  0.00      A   
+ATOM     21  N3  ADE     1       3.091   8.365  -0.708  1.00  0.00      A   
+ATOM     22  C4  ADE     1       2.417   7.202  -0.802  1.00  0.00      A   
+ATOM     23  C6  ADE     1       0.298   8.207  -1.063  1.00  0.00      A   
+ATOM     24  N6  ADE     1      -1.022   8.204  -1.236  1.00  0.00      A   
+ATOM     25  H61 ADE     1      -1.526   9.077  -1.294  1.00  0.00      A   
+ATOM     26  H62 ADE     1      -1.520   7.328  -1.309  1.00  0.00      A   
+ATOM     27  C2' ADE     1       4.646   4.918   0.727  1.00  0.00      A   
+ATOM     28 H2'' ADE     1       4.989   5.649   1.459  1.00  0.00      A   
+ATOM     29  O2' ADE     1       5.086   5.931   1.621  0.00  0.00      A   
+ATOM     30  H2' ADE     1       3.741   4.398   1.062  1.00  0.00      A   
+ATOM     31  C3' ADE     1       5.735   3.930   0.467  1.00  0.00      A   
+ATOM     32  H3' ADE     1       5.546   3.013   1.029  1.00  0.00      A   
+ATOM     33  O3' ADE     1       7.011   4.478   0.823  1.00  0.00      A   
+ATOM     34  P   THY     2       7.364   4.806   2.358  1.00  0.00      A   
+ATOM     35  O1P THY     2       8.839   4.776   2.530  1.00  0.00      A   
+ATOM     36  O2P THY     2       6.515   3.962   3.238  1.00  0.00      A   
+ATOM     37  O5' THY     2       6.861   6.330   2.454  1.00  0.00      A   
+ATOM     38  C5' THY     2       7.276   7.297   1.480  1.00  0.00      A   
+ATOM     39  H5' THY     2       6.804   7.074   0.532  1.00  0.00      A   
+ATOM     40 H5'' THY     2       8.368   7.233   1.371  1.00  0.00      A   
+ATOM     41  C4' THY     2       6.873   8.719   1.849  1.00  0.00      A   
+ATOM     42  H4' THY     2       7.506   9.419   1.306  1.00  0.00      A   
+ATOM     43  O4' THY     2       5.486   8.978   1.507  1.00  0.00      A   
+ATOM     44  C1' THY     2       4.768   9.415   2.684  1.00  0.00      A   
+ATOM     45  H1' THY     2       4.665  10.500   2.653  1.00  0.00      A   
+ATOM     46  N1  THY     2       3.423   8.799   2.747  1.00  0.00      A   
+ATOM     47  C6  THY     2       3.266   7.442   2.852  1.00  0.00      A   
+ATOM     48  H6  THY     2       4.140   6.814   2.982  1.00  0.00      A   
+ATOM     49  C2  THY     2       2.337   9.639   2.626  1.00  0.00      A   
+ATOM     50  O2  THY     2       2.458  10.860   2.552  1.00  0.00      A   
+ATOM     51  N3  THY     2       1.099   9.029   2.606  1.00  0.00      A   
+ATOM     52  H3  THY     2       0.308   9.625   2.509  1.00  0.00      A   
+ATOM     53  C4  THY     2       0.851   7.673   2.697  1.00  0.00      A   
+ATOM     54  O4  THY     2      -0.302   7.243   2.661  1.00  0.00      A   
+ATOM     55  C5  THY     2       2.045   6.871   2.827  1.00  0.00      A   
+ATOM     56  C5M THY     2       1.928   5.354   2.910  1.00  0.00      A   
+ATOM     57  H51 THY     2       1.213   5.085   3.678  1.00  0.00      A   
+ATOM     58  H52 THY     2       2.903   4.926   3.150  1.00  0.00      A   
+ATOM     59  H53 THY     2       1.589   4.964   1.960  1.00  0.00      A   
+ATOM     60  C2' THY     2       5.626   9.038   3.865  1.00  0.00      A   
+ATOM     61 H2'' THY     2       5.564   9.815   4.630  1.00  0.00      A   
+ATOM     62  O2' THY     2       5.490  10.094   4.806  0.00  0.00      A   
+ATOM     63  H2' THY     2       5.324   8.059   4.256  1.00  0.00      A   
+ATOM     64  C3' THY     2       7.025   8.967   3.345  1.00  0.00      A   
+ATOM     65  H3' THY     2       7.553   8.132   3.808  1.00  0.00      A   
+ATOM     66  O3' THY     2       7.719  10.196   3.596  1.00  0.00      A   
+ATOM     67  P   CYT     3       7.980  10.697   5.100  1.00  0.00      A   
+ATOM     68  O1P CYT     3       9.280  11.413   5.150  1.00  0.00      A   
+ATOM     69  O2P CYT     3       7.737   9.569   6.034  1.00  0.00      A   
+ATOM     70  O5' CYT     3       6.789  11.768   5.253  1.00  0.00      A   
+ATOM     71  C5' CYT     3       6.720  12.904   4.380  1.00  0.00      A   
+ATOM     72  H5' CYT     3       6.534  12.568   3.369  1.00  0.00      A   
+ATOM     73 H5'' CYT     3       7.686  13.430   4.420  1.00  0.00      A   
+ATOM     74  C4' CYT     3       5.593  13.866   4.739  1.00  0.00      A   
+ATOM     75  H4' CYT     3       5.709  14.779   4.157  1.00  0.00      A   
+ATOM     76  O4' CYT     3       4.292  13.290   4.450  1.00  0.00      A   
+ATOM     77  C1' CYT     3       3.465  13.339   5.637  1.00  0.00      A   
+ATOM     78  H1' CYT     3       2.791  14.192   5.565  1.00  0.00      A   
+ATOM     79  N1  CYT     3       2.672  12.098   5.790  1.00  0.00      A   
+ATOM     80  C6  CYT     3       3.282  10.889   5.955  1.00  0.00      A   
+ATOM     81  H6  CYT     3       4.365  10.840   6.032  1.00  0.00      A   
+ATOM     82  C5  CYT     3       2.559   9.760   6.045  1.00  0.00      A   
+ATOM     83  H5  CYT     3       3.039   8.789   6.164  1.00  0.00      A   
+ATOM     84  C2  CYT     3       1.294  12.207   5.721  1.00  0.00      A   
+ATOM     85  O2  CYT     3       0.763  13.308   5.588  1.00  0.00      A   
+ATOM     86  N3  CYT     3       0.558  11.072   5.813  1.00  0.00      A   
+ATOM     87  C4  CYT     3       1.140   9.878   5.968  1.00  0.00      A   
+ATOM     88  N4  CYT     3       0.379   8.788   6.044  1.00  0.00      A   
+ATOM     89  H41 CYT     3       0.806   7.880   6.157  1.00  0.00      A   
+ATOM     90  H42 CYT     3      -0.626   8.869   5.991  1.00  0.00      A   
+ATOM     91  C2' CYT     3       4.407  13.552   6.796  1.00  0.00      A   
+ATOM     92 H2'' CYT     3       3.940  14.214   7.534  1.00  0.00      A   
+ATOM     93  O2' CYT     3       3.733  14.417   7.700  0.00  0.00      A   
+ATOM     94  H2' CYT     3       4.689  12.590   7.236  1.00  0.00      A   
+ATOM     95  C3' CYT     3       5.616  14.221   6.221  1.00  0.00      A   
+ATOM     96  H3' CYT     3       6.518  13.815   6.685  1.00  0.00      A   
+ATOM     97  O3' CYT     3       5.555  15.639   6.408  1.00  0.00      A   
+ATOM     98  P   CYT     4       5.538  16.275   7.882  1.00  0.00      A   
+ATOM     99  O1P CYT     4       6.177  17.615   7.835  1.00  0.00      A   
+ATOM    100  O2P CYT     4       6.033  15.266   8.851  1.00  0.00      A   
+ATOM    101  O5' CYT     4       3.955  16.462   8.083  1.00  0.00      A   
+ATOM    102  C5' CYT     4       3.157  17.011   7.025  1.00  0.00      A   
+ATOM    103  H5' CYT     4       3.112  16.305   6.208  1.00  0.00      A   
+ATOM    104 H5'' CYT     4       3.632  17.942   6.682  1.00  0.00      A   
+ATOM    105  C4' CYT     4       1.722  17.289   7.449  1.00  0.00      A   
+ATOM    106  H4' CYT     4       1.321  18.095   6.835  1.00  0.00      A   
+ATOM    107  O4' CYT     4       0.888  16.113   7.280  1.00  0.00      A   
+ATOM    108  C1' CYT     4       0.232  15.803   8.531  1.00  0.00      A   
+ATOM    109  H1' CYT     4      -0.791  16.175   8.498  1.00  0.00      A   
+ATOM    110  N1  CYT     4       0.215  14.343   8.782  1.00  0.00      A   
+ATOM    111  C6  CYT     4       1.375  13.644   8.967  1.00  0.00      A   
+ATOM    112  H6  CYT     4       2.327  14.165   8.951  1.00  0.00      A   
+ATOM    113  C5  CYT     4       1.351  12.313   9.169  1.00  0.00      A   
+ATOM    114  H5  CYT     4       2.272  11.748   9.314  1.00  0.00      A   
+ATOM    115  C2  CYT     4      -1.018  13.712   8.800  1.00  0.00      A   
+ATOM    116  O2  CYT     4      -2.050  14.359   8.636  1.00  0.00      A   
+ATOM    117  N3  CYT     4      -1.049  12.370   9.003  1.00  0.00      A   
+ATOM    118  C4  CYT     4       0.078  11.668   9.183  1.00  0.00      A   
+ATOM    119  N4  CYT     4       0.010  10.348   9.372  1.00  0.00      A   
+ATOM    120  H41 CYT     4       0.855   9.814   9.502  1.00  0.00      A   
+ATOM    121  H42 CYT     4      -0.885   9.881   9.386  1.00  0.00      A   
+ATOM    122  C2' CYT     4       0.992  16.545   9.602  1.00  0.00      A   
+ATOM    123 H2'' CYT     4       0.293  16.923  10.350  1.00  0.00      A   
+ATOM    124  O2' CYT     4       0.020  17.000  10.533  0.00  0.00      A   
+ATOM    125  H2' CYT     4       1.751  15.896  10.049  1.00  0.00      A   
+ATOM    126  C3' CYT     4       1.648  17.697   8.914  1.00  0.00      A   
+ATOM    127  H3' CYT     4       2.656  17.837   9.310  1.00  0.00      A   
+ATOM    128  O3' CYT     4       0.881  18.892   9.085  1.00  0.00      A   
+ATOM    129  P   THY     5       0.647  19.496  10.554  1.00  0.00      A   
+ATOM    130  O1P THY     5       0.561  20.975  10.457  1.00  0.00      A   
+ATOM    131  O2P THY     5       1.626  18.884  11.487  1.00  0.00      A   
+ATOM    132  O5' THY     5      -0.815  18.907  10.868  1.00  0.00      A   
+ATOM    133  C5' THY     5      -1.928  19.273  10.041  1.00  0.00      A   
+ATOM    134  H5' THY     5      -1.694  19.051   9.009  1.00  0.00      A   
+ATOM    135 H5'' THY     5      -2.101  20.352  10.155  1.00  0.00      A   
+ATOM    136  C4' THY     5      -3.200  18.507  10.381  1.00  0.00      A   
+ATOM    137  H4' THY     5      -3.974  18.774   9.662  1.00  0.00      A   
+ATOM    138  O4' THY     5      -2.989  17.071  10.326  1.00  0.00      A   
+ATOM    139  C1' THY     5      -3.410  16.473  11.574  1.00  0.00      A   
+ATOM    140  H1' THY     5      -4.409  16.057  11.449  1.00  0.00      A   
+ATOM    141  N1  THY     5      -2.482  15.396  11.992  1.00  0.00      A   
+ATOM    142  C6  THY     5      -1.153  15.644  12.196  1.00  0.00      A   
+ATOM    143  H6  THY     5      -0.790  16.668  12.147  1.00  0.00      A   
+ATOM    144  C2  THY     5      -3.000  14.117  12.096  1.00  0.00      A   
+ATOM    145  O2  THY     5      -4.196  13.881  11.943  1.00  0.00      A   
+ATOM    146  N3  THY     5      -2.094  13.117  12.403  1.00  0.00      A   
+ATOM    147  H3  THY     5      -2.449  12.182  12.472  1.00  0.00      A   
+ATOM    148  C4  THY     5      -0.742  13.280  12.614  1.00  0.00      A   
+ATOM    149  O4  THY     5      -0.032  12.308  12.873  1.00  0.00      A   
+ATOM    150  C5  THY     5      -0.289  14.648  12.492  1.00  0.00      A   
+ATOM    151  C5M THY     5       1.191  14.967  12.669  1.00  0.00      A   
+ATOM    152  H51 THY     5       1.550  14.530  13.594  1.00  0.00      A   
+ATOM    153  H52 THY     5       1.333  16.047  12.693  1.00  0.00      A   
+ATOM    154  H53 THY     5       1.751  14.549  11.843  1.00  0.00      A   
+ATOM    155  C2' THY     5      -3.465  17.594  12.579  1.00  0.00      A   
+ATOM    156 H2'' THY     5      -4.306  17.435  13.264  1.00  0.00      A   
+ATOM    157  O2' THY     5      -4.580  17.322  13.417  0.00  0.00      A   
+ATOM    158  H2' THY     5      -2.511  17.661  13.116  1.00  0.00      A   
+ATOM    159  C3' THY     5      -3.691  18.844  11.781  1.00  0.00      A   
+ATOM    160  H3' THY     5      -3.096  19.660  12.197  1.00  0.00      A   
+ATOM    161  O3' THY     5      -5.077  19.199  11.761  1.00  0.00      A   
+ATOM    162  P   ADE     6      -5.692  20.169  12.882  1.00  0.00      A   
+ATOM    163  O1P ADE     6      -6.683  21.072  12.244  1.00  0.00      A   
+ATOM    164  O2P ADE     6      -4.583  20.752  13.678  1.00  0.00      A   
+ATOM    165  O5' ADE     6      -6.471  19.094  13.785  1.00  0.00      A   
+ATOM    166  C5' ADE     6      -7.541  18.319  13.232  1.00  0.00      A   
+ATOM    167  H5' ADE     6      -7.211  17.850  12.315  1.00  0.00      A   
+ATOM    168 H5'' ADE     6      -8.386  18.991  13.021  1.00  0.00      A   
+ATOM    169  C4' ADE     6      -7.985  17.203  14.162  1.00  0.00      A   
+ATOM    170  H4' ADE     6      -8.974  16.858  13.863  1.00  0.00      A   
+ATOM    171  O4' ADE     6      -7.060  16.084  14.109  1.00  0.00      A   
+ATOM    172  C1' ADE     6      -6.626  15.770  15.448  1.00  0.00      A   
+ATOM    173  H1' ADE     6      -7.241  14.954  15.831  1.00  0.00      A   
+ATOM    174  N9  ADE     6      -5.206  15.361  15.499  1.00  0.00      A   
+ATOM    175  C5  ADE     6      -3.380  14.152  15.741  1.00  0.00      A   
+ATOM    176  N7  ADE     6      -2.949  15.480  15.662  1.00  0.00      A   
+ATOM    177  C8  ADE     6      -4.070  16.107  15.522  1.00  0.00      A   
+ATOM    178  H8  ADE     6      -4.100  17.190  15.422  1.00  0.00      A   
+ATOM    179  N1  ADE     6      -3.441  11.818  15.931  1.00  0.00      A   
+ATOM    180  C2  ADE     6      -4.769  11.882  15.816  1.00  0.00      A   
+ATOM    181  H2  ADE     6      -5.306  10.937  15.837  1.00  0.00      A   
+ATOM    182  N3  ADE     6      -5.509  12.969  15.668  1.00  0.00      A   
+ATOM    183  C4  ADE     6      -4.749  14.077  15.638  1.00  0.00      A   
+ATOM    184  C6  ADE     6      -2.701  12.939  15.900  1.00  0.00      A   
+ATOM    185  N6  ADE     6      -1.379  12.855  16.045  1.00  0.00      A   
+ATOM    186  H61 ADE     6      -0.941  11.951  16.157  1.00  0.00      A   
+ATOM    187  H62 ADE     6      -0.816  13.693  16.045  1.00  0.00      A   
+ATOM    188  C2' ADE     6      -6.890  17.001  16.274  1.00  0.00      A   
+ATOM    189 H2'' ADE     6      -7.162  16.715  17.291  1.00  0.00      A   
+ATOM    190  O2' ADE     6      -7.256  16.544  17.569  0.00  0.00      A   
+ATOM    191  H2' ADE     6      -6.014  17.659  16.261  1.00  0.00      A   
+ATOM    192  C3' ADE     6      -8.041  17.687  15.608  1.00  0.00      A   
+ATOM    193  H3' ADE     6      -7.903  18.770  15.646  1.00  0.00      A   
+ATOM    194  O3' ADE     6      -9.285  17.318  16.221  1.00  0.00      A   
+ATOM    195  P   GUA     7      -9.843  18.105  17.507  1.00  0.00      A   
+ATOM    196  O1P GUA     7     -11.229  18.561  17.226  1.00  0.00      A   
+ATOM    197  O2P GUA     7      -8.828  19.100  17.939  1.00  0.00      A   
+ATOM    198  O5' GUA     7      -9.897  16.910  18.585  1.00  0.00      A   
+ATOM    199  C5' GUA     7     -10.177  15.560  18.181  1.00  0.00      A   
+ATOM    200  H5' GUA     7      -9.745  15.381  17.207  1.00  0.00      A   
+ATOM    201 H5'' GUA     7     -11.270  15.426  18.114  1.00  0.00      A   
+ATOM    202  C4' GUA     7      -9.561  14.522  19.125  1.00  0.00      A   
+ATOM    203  H4' GUA     7     -10.025  13.556  18.935  1.00  0.00      A   
+ATOM    204  O4' GUA     7      -8.133  14.405  18.887  1.00  0.00      A   
+ATOM    205  C1' GUA     7      -7.410  14.638  20.119  1.00  0.00      A   
+ATOM    206  H1' GUA     7      -7.083  13.684  20.529  1.00  0.00      A   
+ATOM    207  N9  GUA     7      -6.233  15.500  19.896  1.00  0.00      A   
+ATOM    208  C4  GUA     7      -4.911  15.108  19.923  1.00  0.00      A   
+ATOM    209  N2  GUA     7      -2.510  12.617  20.326  1.00  0.00      A   
+ATOM    210  H21 GUA     7      -1.501  12.565  20.299  1.00  0.00      A   
+ATOM    211  H22 GUA     7      -3.053  11.785  20.505  1.00  0.00      A   
+ATOM    212  N3  GUA     7      -4.458  13.854  20.155  1.00  0.00      A   
+ATOM    213  C2  GUA     7      -3.123  13.783  20.119  1.00  0.00      A   
+ATOM    214  N1  GUA     7      -2.305  14.867  19.874  1.00  0.00      A   
+ATOM    215  H1  GUA     7      -1.305  14.730  19.867  1.00  0.00      A   
+ATOM    216  C6  GUA     7      -2.744  16.163  19.632  1.00  0.00      A   
+ATOM    217  O6  GUA     7      -1.932  17.060  19.420  1.00  0.00      A   
+ATOM    218  C5  GUA     7      -4.162  16.248  19.668  1.00  0.00      A   
+ATOM    219  N7  GUA     7      -4.998  17.354  19.481  1.00  0.00      A   
+ATOM    220  C8  GUA     7      -6.168  16.829  19.630  1.00  0.00      A   
+ATOM    221  H8  GUA     7      -7.071  17.433  19.552  1.00  0.00      A   
+ATOM    222  C2' GUA     7      -8.383  15.282  21.074  1.00  0.00      A   
+ATOM    223 H2'' GUA     7      -8.214  14.899  22.086  1.00  0.00      A   
+ATOM    224  O2' GUA     7      -8.103  14.731  22.354  0.00  0.00      A   
+ATOM    225  H2' GUA     7      -8.286  16.373  21.035  1.00  0.00      A   
+ATOM    226  C3' GUA     7      -9.744  14.878  20.608  1.00  0.00      A   
+ATOM    227  H3' GUA     7     -10.429  15.719  20.727  1.00  0.00      A   
+ATOM    228  O3' GUA     7     -10.214  13.747  21.352  1.00  0.00      A   
+ATOM    229  P   THY     8     -10.470  13.861  22.933  1.00  0.00      A   
+ATOM    230  O1P THY     8     -11.662  13.049  23.287  1.00  0.00      A   
+ATOM    231  O2P THY     8     -10.423  15.292  23.326  1.00  0.00      A   
+ATOM    232  O5' THY     8      -9.152  13.125  23.489  1.00  0.00      A   
+ATOM    233  C5' THY     8      -9.105  11.695  23.588  1.00  0.00      A   
+ATOM    234  H5' THY     8      -9.468  11.262  22.666  1.00  0.00      A   
+ATOM    235 H5'' THY     8      -9.754  11.381  24.418  1.00  0.00      A   
+ATOM    236  C4' THY     8      -7.687  11.168  23.791  1.00  0.00      A   
+ATOM    237  H4' THY     8      -7.609  10.181  23.338  1.00  0.00      A   
+ATOM    238  O4' THY     8      -6.715  12.044  23.168  1.00  0.00      A   
+ATOM    239  C1' THY     8      -5.719  12.435  24.137  1.00  0.00      A   
+ATOM    240  H1' THY     8      -4.826  11.809  24.000  1.00  0.00      A   
+ATOM    241  N1  THY     8      -5.347  13.860  23.988  1.00  0.00      A   
+ATOM    242  C6  THY     8      -6.259  14.865  24.197  1.00  0.00      A   
+ATOM    243  H6  THY     8      -7.285  14.614  24.463  1.00  0.00      A   
+ATOM    244  C2  THY     8      -4.038  14.136  23.637  1.00  0.00      A   
+ATOM    245  O2  THY     8      -3.212  13.247  23.443  1.00  0.00      A   
+ATOM    246  N3  THY     8      -3.711  15.473  23.513  1.00  0.00      A   
+ATOM    247  H3  THY     8      -2.758  15.688  23.257  1.00  0.00      A   
+ATOM    248  C4  THY     8      -4.564  16.543  23.707  1.00  0.00      A   
+ATOM    249  O4  THY     8      -4.163  17.697  23.570  1.00  0.00      A   
+ATOM    250  C5  THY     8      -5.910  16.163  24.071  1.00  0.00      A   
+ATOM    251  C5M THY     8      -6.952  17.250  24.322  1.00  0.00      A   
+ATOM    252  H51 THY     8      -7.951  16.823  24.241  1.00  0.00      A   
+ATOM    253  H52 THY     8      -6.834  18.044  23.584  1.00  0.00      A   
+ATOM    254  H53 THY     8      -6.813  17.662  25.322  1.00  0.00      A   
+ATOM    255  C2' THY     8      -6.324  12.155  25.493  1.00  0.00      A   
+ATOM    256 H2'' THY     8      -5.551  11.817  26.188  1.00  0.00      A   
+ATOM    257  O2' THY     8      -5.259  11.702  26.317  0.00  0.00      A   
+ATOM    258  H2' THY     8      -6.834  13.050  25.864  1.00  0.00      A   
+ATOM    259  C3' THY     8      -7.326  11.065  25.272  1.00  0.00      A   
+ATOM    260  H3' THY     8      -8.207  11.245  25.890  1.00  0.00      A   
+ATOM    261  O3' THY     8      -6.760   9.782  25.572  1.00  0.00      A   
+ATOM    262  P   THY     9      -6.511   9.330  27.094  1.00  0.00      A   
+ATOM    263  O1P THY     9      -6.391   7.851  27.145  1.00  0.00      A   
+ATOM    264  O2P THY     9      -7.505  10.007  27.965  1.00  0.00      A   
+ATOM    265  O5' THY     9      -5.064   9.980  27.352  1.00  0.00      A   
+ATOM    266  C5' THY     9      -3.880   9.385  26.799  1.00  0.00      A   
+ATOM    267  H5' THY     9      -4.151   8.500  26.239  1.00  0.00      A   
+ATOM    268 H5'' THY     9      -3.212   9.106  27.628  1.00  0.00      A   
+ATOM    269  C4' THY     9      -3.160  10.317  25.831  1.00  0.00      A   
+ATOM    270  H4' THY     9      -3.569  10.180  24.831  1.00  0.00      A   
+ATOM    271  O4' THY     9      -3.322  11.705  26.223  1.00  0.00      A   
+ATOM    272  C1' THY     9      -2.022  12.314  26.402  1.00  0.00      A   
+ATOM    273  H1' THY     9      -1.789  12.931  25.535  1.00  0.00      A   
+ATOM    274  N1  THY     9      -1.980  13.144  27.620  1.00  0.00      A   
+ATOM    275  C6  THY     9      -2.301  12.617  28.841  1.00  0.00      A   
+ATOM    276  H6  THY     9      -2.602  11.572  28.910  1.00  0.00      A   
+ATOM    277  C2  THY     9      -1.594  14.462  27.479  1.00  0.00      A   
+ATOM    278  O2  THY     9      -1.304  14.946  26.388  1.00  0.00      A   
+ATOM    279  N3  THY     9      -1.550  15.208  28.642  1.00  0.00      A   
+ATOM    280  H3  THY     9      -1.266  16.173  28.556  1.00  0.00      A   
+ATOM    281  C4  THY     9      -1.856  14.754  29.913  1.00  0.00      A   
+ATOM    282  O4  THY     9      -1.781  15.506  30.882  1.00  0.00      A   
+ATOM    283  C5  THY     9      -2.250  13.364  29.961  1.00  0.00      A   
+ATOM    284  C5M THY     9      -2.613  12.733  31.301  1.00  0.00      A   
+ATOM    285  H51 THY     9      -3.440  13.282  31.750  1.00  0.00      A   
+ATOM    286  H52 THY     9      -1.749  12.768  31.965  1.00  0.00      A   
+ATOM    287  H53 THY     9      -2.907  11.695  31.144  1.00  0.00      A   
+ATOM    288  C2' THY     9      -1.031  11.183  26.492  1.00  0.00      A   
+ATOM    289 H2'' THY     9      -0.104  11.461  25.976  1.00  0.00      A   
+ATOM    290  O2' THY     9       0.130  11.618  25.797  0.00  0.00      A   
+ATOM    291  H2' THY     9      -0.850  10.929  27.544  1.00  0.00      A   
+ATOM    292  C3' THY     9      -1.667  10.028  25.792  1.00  0.00      A   
+ATOM    293  H3' THY     9      -1.452   9.104  26.331  1.00  0.00      A   
+ATOM    294  O3' THY     9      -1.201   9.937  24.447  1.00  0.00      A   
+ATOM    295  P   ADE    10      -0.315   8.688  23.992  1.00  0.00      A   
+ATOM    296  O1P ADE    10       0.551   8.277  25.125  1.00  0.00      A   
+ATOM    297  O2P ADE    10       0.304   8.985  22.676  1.00  0.00      A   
+ATOM    298  O5' ADE    10      -1.467   7.588  23.799  1.00  0.00      A   
+ATOM    299  C5' ADE    10      -1.147   6.209  23.981  1.00  0.00      A   
+ATOM    300  H5' ADE    10      -1.499   5.914  24.943  1.00  0.00      A   
+ATOM    301 H5'' ADE    10      -0.058   6.091  23.938  1.00  0.00      A   
+ATOM    302  C4' ADE    10      -1.836   5.303  22.968  1.00  0.00      A   
+ATOM    303  H4' ADE    10      -2.067   4.345  23.431  1.00  0.00      A   
+ATOM    304  O4' ADE    10      -3.058   5.912  22.482  1.00  0.00      A   
+ATOM    305  C1' ADE    10      -2.814   6.401  21.156  1.00  0.00      A   
+ATOM    306  H1' ADE    10      -3.405   5.820  20.462  1.00  0.00      A   
+ATOM    307  N9  ADE    10      -3.245   7.804  21.056  1.00  0.00      A   
+ATOM    308  C5  ADE    10      -4.488   9.625  21.105  1.00  0.00      A   
+ATOM    309  N7  ADE    10      -3.166  10.059  21.189  1.00  0.00      A   
+ATOM    310  C8  ADE    10      -2.525   8.939  21.164  1.00  0.00      A   
+ATOM    311  H8  ADE    10      -1.467   8.901  21.352  1.00  0.00      A   
+ATOM    312  N1  ADE    10      -6.829   9.568  20.995  1.00  0.00      A   
+ATOM    313  C2  ADE    10      -6.756   8.238  20.930  1.00  0.00      A   
+ATOM    314  H2  ADE    10      -7.703   7.703  20.862  1.00  0.00      A   
+ATOM    315  N3  ADE    10      -5.655   7.493  20.942  1.00  0.00      A   
+ATOM    316  C4  ADE    10      -4.547   8.257  21.031  1.00  0.00      A   
+ATOM    317  C6  ADE    10      -5.708  10.306  21.082  1.00  0.00      A   
+ATOM    318  N6  ADE    10      -5.798  11.634  21.109  1.00  0.00      A   
+ATOM    319  H61 ADE    10      -4.961  12.197  21.148  1.00  0.00      A   
+ATOM    320  H62 ADE    10      -6.705  12.077  21.097  1.00  0.00      A   
+ATOM    321  C2' ADE    10      -1.353   6.163  20.832  1.00  0.00      A   
+ATOM    322 H2'' ADE    10      -1.255   5.812  19.797  1.00  0.00      A   
+ATOM    323  O2' ADE    10      -1.304   5.706  19.487  0.00  0.00      A   
+ATOM    324  H2' ADE    10      -0.763   7.061  21.013  1.00  0.00      A   
+ATOM    325  C3' ADE    10      -0.922   5.089  21.772  1.00  0.00      A   
+ATOM    326  H3' ADE    10       0.123   5.233  22.050  1.00  0.00      A   
+ATOM    327  O3' ADE    10      -1.116   3.794  21.200  1.00  0.00      A   
+ATOM    328  P   THY    11      -0.300   3.354  19.891  1.00  0.00      A   
+ATOM    329  O1P THY    11       0.097   1.930  20.024  1.00  0.00      A   
+ATOM    330  O2P THY    11       0.734   4.378  19.599  1.00  0.00      A   
+ATOM    331  O5' THY    11      -1.473   3.469  18.803  1.00  0.00      A   
+ATOM    332  C5' THY    11      -2.662   2.689  18.966  1.00  0.00      A   
+ATOM    333  H5' THY    11      -2.944   2.680  20.010  1.00  0.00      A   
+ATOM    334 H5'' THY    11      -2.451   1.662  18.634  1.00  0.00      A   
+ATOM    335  C4' THY    11      -3.851   3.245  18.197  1.00  0.00      A   
+ATOM    336  H4' THY    11      -4.766   2.847  18.632  1.00  0.00      A   
+ATOM    337  O4' THY    11      -3.901   4.696  18.258  1.00  0.00      A   
+ATOM    338  C1' THY    11      -4.030   5.228  16.919  1.00  0.00      A   
+ATOM    339  H1' THY    11      -5.080   5.439  16.719  1.00  0.00      A   
+ATOM    340  N1  THY    11      -3.239   6.466  16.744  1.00  0.00      A   
+ATOM    341  C6  THY    11      -1.881   6.470  16.918  1.00  0.00      A   
+ATOM    342  H6  THY    11      -1.372   5.540  17.168  1.00  0.00      A   
+ATOM    343  C2  THY    11      -3.928   7.616  16.410  1.00  0.00      A   
+ATOM    344  O2  THY    11      -5.147   7.627  16.255  1.00  0.00      A   
+ATOM    345  N3  THY    11      -3.167   8.760  16.267  1.00  0.00      A   
+ATOM    346  H3  THY    11      -3.656   9.597  16.002  1.00  0.00      A   
+ATOM    347  C4  THY    11      -1.796   8.854  16.430  1.00  0.00      A   
+ATOM    348  O4  THY    11      -1.220   9.932  16.292  1.00  0.00      A   
+ATOM    349  C5  THY    11      -1.161   7.602  16.776  1.00  0.00      A   
+ATOM    350  C5M THY    11       0.348   7.560  16.990  1.00  0.00      A   
+ATOM    351  H51 THY    11       0.804   8.445  16.550  1.00  0.00      A   
+ATOM    352  H52 THY    11       0.757   6.667  16.526  1.00  0.00      A   
+ATOM    353  H53 THY    11       0.561   7.538  18.049  1.00  0.00      A   
+ATOM    354  C2' THY    11      -3.564   4.136  15.992  1.00  0.00      A   
+ATOM    355 H2'' THY    11      -4.165   4.148  15.075  1.00  0.00      A   
+ATOM    356  O2' THY    11      -4.394   4.212  14.841  0.00  0.00      A   
+ATOM    357  H2' THY    11      -2.495   4.258  15.779  1.00  0.00      A   
+ATOM    358  C3' THY    11      -3.793   2.852  16.729  1.00  0.00      A   
+ATOM    359  H3' THY    11      -2.953   2.176  16.559  1.00  0.00      A   
+ATOM    360  O3' THY    11      -5.015   2.233  16.322  1.00  0.00      A   
+ATOM    361  P   ADE    12      -5.221   1.752  14.807  1.00  0.00      A   
+ATOM    362  O1P ADE    12      -6.125   0.574  14.792  1.00  0.00      A   
+ATOM    363  O2P ADE    12      -3.895   1.663  14.146  1.00  0.00      A   
+ATOM    364  O5' ADE    12      -6.010   3.023  14.225  1.00  0.00      A   
+ATOM    365  C5' ADE    12      -7.077   3.615  14.980  1.00  0.00      A   
+ATOM    366  H5' ADE    12      -6.670   4.100  15.857  1.00  0.00      A   
+ATOM    367 H5'' ADE    12      -7.769   2.818  15.287  1.00  0.00      A   
+ATOM    368  C4' ADE    12      -7.824   4.680  14.194  1.00  0.00      A   
+ATOM    369  H4' ADE    12      -8.830   4.786  14.598  1.00  0.00      A   
+ATOM    370  O4' ADE    12      -7.144   5.958  14.280  1.00  0.00      A   
+ATOM    371  C1' ADE    12      -6.790   6.408  12.952  1.00  0.00      A   
+ATOM    372  H1' ADE    12      -7.490   7.183  12.639  1.00  0.00      A   
+ATOM    373  N9  ADE    12      -5.417   6.949  12.917  1.00  0.00      A   
+ATOM    374  C5  ADE    12      -3.693   8.321  12.830  1.00  0.00      A   
+ATOM    375  N7  ADE    12      -3.157   7.043  13.020  1.00  0.00      A   
+ATOM    376  C8  ADE    12      -4.226   6.316  13.057  1.00  0.00      A   
+ATOM    377  H8  ADE    12      -4.171   5.237  13.186  1.00  0.00      A   
+ATOM    378  N1  ADE    12      -3.941  10.629  12.522  1.00  0.00      A   
+ATOM    379  C2  ADE    12      -5.257  10.448  12.476  1.00  0.00      A   
+ATOM    380  H2  ADE    12      -5.861  11.340  12.337  1.00  0.00      A   
+ATOM    381  N3  ADE    12      -5.913   9.300  12.587  1.00  0.00      A   
+ATOM    382  C4  ADE    12      -5.067   8.268  12.764  1.00  0.00      A   
+ATOM    383  C6  ADE    12      -3.111   9.589  12.699  1.00  0.00      A   
+ATOM    384  N6  ADE    12      -1.795   9.805  12.753  1.00  0.00      A   
+ATOM    385  H61 ADE    12      -1.162   9.032  12.894  1.00  0.00      A   
+ATOM    386  H62 ADE    12      -1.429  10.745  12.648  1.00  0.00      A   
+ATOM    387  C2' ADE    12      -6.935   5.215  12.045  1.00  0.00      A   
+ATOM    388 H2'' ADE    12      -7.341   5.533  11.081  1.00  0.00      A   
+ATOM    389  O2' ADE    12      -7.468   5.708  10.823  0.00  0.00      A   
+ATOM    390  H2' ADE    12      -5.967   4.711  11.933  1.00  0.00      A   
+ATOM    391  C3' ADE    12      -7.909   4.308  12.721  1.00  0.00      A   
+ATOM    392  H3' ADE    12      -7.606   3.268  12.582  1.00  0.00      A   
+ATOM    393  O3' ADE    12      -9.231   4.514  12.212  1.00  0.00      A   
+ATOM    394  P   GUA    13      -9.569   4.219  10.669  1.00  0.00      A   
+ATOM    395  O1P GUA    13     -10.964   3.722  10.568  1.00  0.00      A   
+ATOM    396  O2P GUA    13      -8.467   3.416  10.078  1.00  0.00      A   
+ATOM    397  O5' GUA    13      -9.502   5.712  10.074  1.00  0.00      A   
+ATOM    398  C5' GUA    13     -10.262   6.771  10.674  1.00  0.00      A   
+ATOM    399  H5' GUA    13      -9.915   6.931  11.687  1.00  0.00      A   
+ATOM    400 H5'' GUA    13     -11.321   6.472  10.690  1.00  0.00      A   
+ATOM    401  C4' GUA    13     -10.106   8.098   9.939  1.00  0.00      A   
+ATOM    402  H4' GUA    13     -10.856   8.800  10.304  1.00  0.00      A   
+ATOM    403  O4' GUA    13      -8.786   8.662  10.158  1.00  0.00      A   
+ATOM    404  C1' GUA    13      -8.107   8.815   8.888  1.00  0.00      A   
+ATOM    405  H1' GUA    13      -8.123   9.865   8.595  1.00  0.00      A   
+ATOM    406  N9  GUA    13      -6.709   8.354   8.973  1.00  0.00      A   
+ATOM    407  C4  GUA    13      -5.588   9.146   8.985  1.00  0.00      A   
+ATOM    408  N2  GUA    13      -4.124  12.296   8.784  1.00  0.00      A   
+ATOM    409  H21 GUA    13      -3.184  12.667   8.819  1.00  0.00      A   
+ATOM    410  H22 GUA    13      -4.906  12.918   8.649  1.00  0.00      A   
+ATOM    411  N3  GUA    13      -5.570  10.492   8.868  1.00  0.00      A   
+ATOM    412  C2  GUA    13      -4.330  10.984   8.915  1.00  0.00      A   
+ATOM    413  N1  GUA    13      -3.206  10.202   9.073  1.00  0.00      A   
+ATOM    414  H1  GUA    13      -2.315  10.646   9.124  1.00  0.00      A   
+ATOM    415  C6  GUA    13      -3.197   8.821   9.193  1.00  0.00      A   
+ATOM    416  O6  GUA    13      -2.131   8.221   9.329  1.00  0.00      A   
+ATOM    417  C5  GUA    13      -4.509   8.289   9.140  1.00  0.00      A   
+ATOM    418  N7  GUA    13      -4.941   6.963   9.220  1.00  0.00      A   
+ATOM    419  C8  GUA    13      -6.219   7.099   9.112  1.00  0.00      A   
+ATOM    420  H8  GUA    13      -6.878   6.234   9.115  1.00  0.00      A   
+ATOM    421  C2' GUA    13      -8.891   8.009   7.886  1.00  0.00      A   
+ATOM    422 H2'' GUA    13      -8.913   8.529   6.925  1.00  0.00      A   
+ATOM    423  O2' GUA    13      -8.878   8.756   6.677  0.00  0.00      A   
+ATOM    424  H2' GUA    13      -8.460   7.004   7.796  1.00  0.00      A   
+ATOM    425  C3' GUA    13     -10.275   7.918   8.438  1.00  0.00      A   
+ATOM    426  H3' GUA    13     -10.699   6.935   8.226  1.00  0.00      A   
+ATOM    427  O3' GUA    13     -11.101   8.949   7.886  1.00  0.00      A   
+ATOM    428  P   GUA    14     -11.390   9.003   6.307  1.00  0.00      A   
+ATOM    429  O1P GUA    14     -12.822   9.326   6.088  1.00  0.00      A   
+ATOM    430  O2P GUA    14     -10.812   7.792   5.669  1.00  0.00      A   
+ATOM    431  O5' GUA    14     -10.498  10.281   5.903  1.00  0.00      A   
+ATOM    432  C5' GUA    14     -10.655  11.527   6.598  1.00  0.00      A   
+ATOM    433  H5' GUA    14     -10.451  11.380   7.649  1.00  0.00      A   
+ATOM    434 H5'' GUA    14     -11.694  11.866   6.469  1.00  0.00      A   
+ATOM    435  C4' GUA    14      -9.695  12.606   6.108  1.00  0.00      A   
+ATOM    436  H4' GUA    14     -10.002  13.566   6.522  1.00  0.00      A   
+ATOM    437  O4' GUA    14      -8.331  12.331   6.524  1.00  0.00      A   
+ATOM    438  C1' GUA    14      -7.466  12.306   5.364  1.00  0.00      A   
+ATOM    439  H1' GUA    14      -6.929  13.252   5.293  1.00  0.00      A   
+ATOM    440  N9  GUA    14      -6.496  11.197   5.439  1.00  0.00      A   
+ATOM    441  C4  GUA    14      -5.130  11.309   5.503  1.00  0.00      A   
+ATOM    442  N2  GUA    14      -2.272  13.284   5.569  1.00  0.00      A   
+ATOM    443  H21 GUA    14      -1.276  13.122   5.619  1.00  0.00      A   
+ATOM    444  H22 GUA    14      -2.629  14.227   5.521  1.00  0.00      A   
+ATOM    445  N3  GUA    14      -4.431  12.464   5.499  1.00  0.00      A   
+ATOM    446  C2  GUA    14      -3.115  12.253   5.569  1.00  0.00      A   
+ATOM    447  N1  GUA    14      -2.546  11.000   5.639  1.00  0.00      A   
+ATOM    448  H1  GUA    14      -1.553  10.927   5.697  1.00  0.00      A   
+ATOM    449  C6  GUA    14      -3.243   9.800   5.643  1.00  0.00      A   
+ATOM    450  O6  GUA    14      -2.637   8.733   5.710  1.00  0.00      A   
+ATOM    451  C5  GUA    14      -4.640  10.014   5.568  1.00  0.00      A   
+ATOM    452  N7  GUA    14      -5.685   9.089   5.544  1.00  0.00      A   
+ATOM    453  C8  GUA    14      -6.712   9.862   5.468  1.00  0.00      A   
+ATOM    454  H8  GUA    14      -7.718   9.456   5.407  1.00  0.00      A   
+ATOM    455  C2' GUA    14      -8.370  12.156   4.168  1.00  0.00      A   
+ATOM    456 H2'' GUA    14      -7.981  12.746   3.333  1.00  0.00      A   
+ATOM    457  O2' GUA    14      -7.800  12.955   3.140  0.00  0.00      A   
+ATOM    458  H2' GUA    14      -8.468  11.095   3.906  1.00  0.00      A   
+ATOM    459  C3' GUA    14      -9.699  12.699   4.588  1.00  0.00      A   
+ATOM    460  H3' GUA    14     -10.498  12.075   4.180  1.00  0.00      A   
+ATOM    461  O3' GUA    14      -9.858  14.054   4.155  1.00  0.00      A   
+ATOM    462  P   ADE    15      -9.872  14.418   2.591  1.00  0.00      A   
+ATOM    463  O1P ADE    15     -10.717  15.621   2.385  1.00  0.00      A   
+ATOM    464  O2P ADE    15     -10.159  13.187   1.811  1.00  0.00      A   
+ATOM    465  O5' ADE    15      -8.329  14.822   2.384  1.00  0.00      A   
+ATOM    466  C5' ADE    15      -7.757  15.905   3.132  1.00  0.00      A   
+ATOM    467  H5' ADE    15      -7.679  15.620   4.173  1.00  0.00      A   
+ATOM    468 H5'' ADE    15      -8.419  16.778   3.038  1.00  0.00      A   
+ATOM    469  C4' ADE    15      -6.352  16.267   2.666  1.00  0.00      A   
+ATOM    470  H4' ADE    15      -6.074  17.231   3.090  1.00  0.00      A   
+ATOM    471  O4' ADE    15      -5.384  15.271   3.088  1.00  0.00      A   
+ATOM    472  C1' ADE    15      -4.683  14.758   1.931  1.00  0.00      A   
+ATOM    473  H1' ADE    15      -3.701  15.229   1.864  1.00  0.00      A   
+ATOM    474  N9  ADE    15      -4.519  13.297   2.002  1.00  0.00      A   
+ATOM    475  C5  ADE    15      -3.661  11.277   2.155  1.00  0.00      A   
+ATOM    476  N7  ADE    15      -5.037  11.096   2.004  1.00  0.00      A   
+ATOM    477  C8  ADE    15      -5.449  12.315   1.922  1.00  0.00      A   
+ATOM    478  H8  ADE    15      -6.501  12.547   1.781  1.00  0.00      A   
+ATOM    479  N1  ADE    15      -1.372  10.906   2.425  1.00  0.00      A   
+ATOM    480  C2  ADE    15      -1.189  12.224   2.412  1.00  0.00      A   
+ATOM    481  H2  ADE    15      -0.165  12.572   2.528  1.00  0.00      A   
+ATOM    482  N3  ADE    15      -2.117  13.160   2.280  1.00  0.00      A   
+ATOM    483  C4  ADE    15      -3.341  12.615   2.156  1.00  0.00      A   
+ATOM    484  C6  ADE    15      -2.600  10.384   2.299  1.00  0.00      A   
+ATOM    485  N6  ADE    15      -2.755   9.059   2.312  1.00  0.00      A   
+ATOM    486  H61 ADE    15      -1.949   8.456   2.417  1.00  0.00      A   
+ATOM    487  H62 ADE    15      -3.677   8.658   2.219  1.00  0.00      A   
+ATOM    488  C2' ADE    15      -5.504  15.149   0.731  1.00  0.00      A   
+ATOM    489 H2'' ADE    15      -4.844  15.409  -0.102  1.00  0.00      A   
+ATOM    490  O2' ADE    15      -4.576  15.478  -0.294  0.00  0.00      A   
+ATOM    491  H2' ADE    15      -6.190  14.335   0.468  1.00  0.00      A   
+ATOM    492  C3' ADE    15      -6.283  16.352   1.147  1.00  0.00      A   
+ATOM    493  H3' ADE    15      -7.289  16.303   0.726  1.00  0.00      A   
+ATOM    494  O3' ADE    15      -5.624  17.548   0.722  1.00  0.00      A   
+ATOM    495  P   THY    16      -5.398  17.836  -0.841  1.00  0.00      A   
+ATOM    496  O1P THY    16      -5.436  19.302  -1.072  1.00  0.00      A   
+ATOM    497  O2P THY    16      -6.293  16.951  -1.628  1.00  0.00      A   
+ATOM    498  O5' THY    16      -3.882  17.322  -1.001  1.00  0.00      A   
+ATOM    499  C5' THY    16      -2.838  17.907  -0.211  1.00  0.00      A   
+ATOM    500  H5' THY    16      -2.999  17.667   0.830  1.00  0.00      A   
+ATOM    501 H5'' THY    16      -2.874  18.998  -0.347  1.00  0.00      A   
+ATOM    502  C4' THY    16      -1.452  17.388  -0.574  1.00  0.00      A   
+ATOM    503  H4' THY    16      -0.705  17.995  -0.065  1.00  0.00      A   
+ATOM    504  O4' THY    16      -1.281  16.003  -0.170  1.00  0.00      A   
+ATOM    505  C1' THY    16      -0.834  15.221  -1.300  1.00  0.00      A   
+ATOM    506  H1' THY    16       0.246  15.085  -1.238  1.00  0.00      A   
+ATOM    507  N1  THY    16      -1.493  13.897  -1.332  1.00  0.00      A   
+ATOM    508  C6  THY    16      -2.847  13.782  -1.508  1.00  0.00      A   
+ATOM    509  H6  THY    16      -3.452  14.681  -1.599  1.00  0.00      A   
+ATOM    510  C2  THY    16      -0.686  12.781  -1.194  1.00  0.00      A   
+ATOM    511  O2  THY    16       0.530  12.869  -1.037  1.00  0.00      A   
+ATOM    512  N3  THY    16      -1.328  11.558  -1.246  1.00  0.00      A   
+ATOM    513  H3  THY    16      -0.760  10.742  -1.134  1.00  0.00      A   
+ATOM    514  C4  THY    16      -2.685  11.356  -1.424  1.00  0.00      A   
+ATOM    515  O4  THY    16      -3.150  10.219  -1.466  1.00  0.00      A   
+ATOM    516  C5  THY    16      -3.447  12.577  -1.557  1.00  0.00      A   
+ATOM    517  C5M THY    16      -4.957  12.501  -1.760  1.00  0.00      A   
+ATOM    518  H51 THY    16      -5.422  13.407  -1.376  1.00  0.00      A   
+ATOM    519  H52 THY    16      -5.352  11.634  -1.237  1.00  0.00      A   
+ATOM    520  H53 THY    16      -5.176  12.408  -2.814  1.00  0.00      A   
+ATOM    521  C2' THY    16      -1.160  16.036  -2.531  1.00  0.00      A   
+ATOM    522 H2'' THY    16      -0.365  15.912  -3.277  1.00  0.00      A   
+ATOM    523  O2' THY    16      -0.085  15.830  -3.438  0.00  0.00      A   
+ATOM    524  H2' THY    16      -2.137  15.741  -2.930  1.00  0.00      A   
+ATOM    525  C3' THY    16      -1.207  17.463  -2.076  1.00  0.00      A   
+ATOM    526  H3' THY    16      -2.043  17.975  -2.561  1.00  0.00      A   
+ATOM    527  O3' THY    16       0.021  18.138  -2.365  1.00  0.00      A   
+END

tools/ch2lmp/example/1ac7.pgn

@@ -0,0 +1,81 @@
+package require psfgen   
+topology top_all27_na.rtf
+pdbalias residue A ADE 
+pdbalias residue T THY 
+pdbalias residue G GUA 
+pdbalias residue C CYT 
+pdbalias atom ADE O3* O3'
+pdbalias atom THY O3* O3'
+pdbalias atom GUA O3* O3'
+pdbalias atom CYT O3* O3'
+pdbalias atom ADE O4* O4'
+pdbalias atom THY O4* O4'
+pdbalias atom GUA O4* O4'
+pdbalias atom CYT O4* O4'
+pdbalias atom ADE O5* O5'
+pdbalias atom THY O5* O5'
+pdbalias atom GUA O5* O5'
+pdbalias atom CYT O5* O5'
+pdbalias atom ADE C1* C1'
+pdbalias atom THY C1* C1'
+pdbalias atom GUA C1* C1'
+pdbalias atom CYT C1* C1'
+pdbalias atom ADE C2* C2'
+pdbalias atom THY C2* C2'
+pdbalias atom GUA C2* C2'
+pdbalias atom CYT C2* C2'
+pdbalias atom ADE C3* C3'
+pdbalias atom THY C3* C3'
+pdbalias atom GUA C3* C3'
+pdbalias atom CYT C3* C3'
+pdbalias atom ADE C4* C4'
+pdbalias atom THY C4* C4'
+pdbalias atom GUA C4* C4'
+pdbalias atom CYT C4* C4'
+pdbalias atom ADE C5* C5'
+pdbalias atom THY C5* C5'
+pdbalias atom GUA C5* C5'
+pdbalias atom CYT C5* C5'
+pdbalias atom ADE H1* H1'
+pdbalias atom THY H1* H1'
+pdbalias atom GUA H1* H1'
+pdbalias atom CYT H1* H1'
+pdbalias atom ADE H3* H3'
+pdbalias atom THY H3* H3'
+pdbalias atom GUA H3* H3'
+pdbalias atom CYT H3* H3'
+pdbalias atom ADE H4* H4'
+pdbalias atom THY H4* H4'
+pdbalias atom GUA H4* H4'
+pdbalias atom CYT H4* H4'
+pdbalias atom ADE 1H5* H5'
+pdbalias atom THY 1H5* H5'
+pdbalias atom GUA 1H5* H5'
+pdbalias atom CYT 1H5* H5'
+pdbalias atom ADE 2H5* H5''
+pdbalias atom THY 2H5* H5''
+pdbalias atom GUA 2H5* H5''
+pdbalias atom CYT 2H5* H5''
+pdbalias atom ADE 1H2* H2'
+pdbalias atom THY 1H2* H2'
+pdbalias atom GUA 1H2* H2'
+pdbalias atom CYT 1H2* H2'
+pdbalias atom ADE 2H2* H2''
+pdbalias atom THY 2H2* H2''
+pdbalias atom GUA 2H2* H2''
+pdbalias atom CYT 2H2* H2''
+pdbalias atom GUA 1H2 H21
+pdbalias atom GUA 2H2 H22
+pdbalias atom CYT 1H4 H41
+pdbalias atom CYT 2H4 H42
+pdbalias atom ADE 1H6 H61
+pdbalias atom ADE 2H6 H62
+pdbalias atom THY 1H5M H51
+pdbalias atom THY 2H5M H52
+pdbalias atom THY 3H5M H53
+segment A {pdb 1ac7_pared.pdb}   
+coordpdb 1ac7_pared.pdb A   
+guesscoord   
+writepdb 1ac7.pdb   
+writepsf charmm 1ac7.psf  
+exit 

tools/ch2lmp/example/1ac7_pared.pdb

@@ -0,0 +1,540 @@
+HEADER    DNA                                     14-FEB-97   XXXX              
+TITLE     STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT):           
+TITLE    2 THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10                
+TITLE    3 STRUCTURES                                                           
+COMPND    5'-D(*AP*TP*CP*CP*TP*AP*GP*TP*TP*AP*TP*AP*GP*GP*AP*T)-3'              
+KEYWDS    DEOXYRIBONUCLEIC ACID                                                 
+EXPDTA    NMR, 10 STRUCTURES                                                    
+AUTHOR    M.J.P.VAN DONGEN, M.M.W.MOOREN, E.F.A.WILLEMS, G.A.VAN DER            
+AUTHOR   2 MAREL, J.H.VAN BOOM, S.S.WIJMENGA, C.W.HILBERS                       
+JRNL        AUTH   M.J.VAN DONGEN, M.M.MOOREN, E.F.WILLEMS,                     
+JRNL        AUTH 2 G.A.VAN DER MAREL, J.H.VAN BOOM, S.S.WIJMENGA,               
+JRNL        AUTH 3 C.W.HILBERS                                                  
+JRNL        TITL   STRUCTURAL FEATURES OF THE DNA HAIRPIN                       
+JRNL        TITL 2 D(ATCCTA-GTTA-TAGGAT): FORMATION OF A G-A BASE               
+JRNL        TITL 3 PAIR IN THE LOOP                                             
+JRNL        REF    NUCLEIC ACIDS RES.            V.  25  1537 1997              
+JRNL        REFN   ASTM NARHAD  UK ISSN 0305-1048                               
+REMARK   1                                                                      
+SEQRES   1 A   16    A   T   C   C   T   A   G   T   T   A   T   A   G          
+SEQRES   2 A   16    G   A   T                                                  
+CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      1.000000  0.000000  0.000000        0.00000                         
+SCALE2      0.000000  1.000000  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  1.000000        0.00000                         
+MODEL        1                                                                  
+ATOM      1  O5*   A A   1       3.969   1.972  -0.393  1.00  0.00           O  
+ATOM      2  C5*   A A   1       5.044   2.279  -1.290  1.00  0.00           C  
+ATOM      3  C4*   A A   1       5.648   3.651  -1.028  1.00  0.00           C  
+ATOM      4  O4*   A A   1       4.831   4.694  -1.619  1.00  0.00           O  
+ATOM      5  C3*   A A   1       5.735   3.930   0.467  1.00  0.00           C  
+ATOM      6  O3*   A A   1       7.011   4.478   0.823  1.00  0.00           O  
+ATOM      7  C2*   A A   1       4.646   4.918   0.727  1.00  0.00           C  
+ATOM      8  C1*   A A   1       4.388   5.605  -0.589  1.00  0.00           C  
+ATOM      9  N9    A A   1       2.960   5.940  -0.745  1.00  0.00           N  
+ATOM     10  C8    A A   1       1.887   5.123  -0.884  1.00  0.00           C  
+ATOM     11  N7    A A   1       0.730   5.679  -1.026  1.00  0.00           N  
+ATOM     12  C5    A A   1       1.063   7.037  -0.974  1.00  0.00           C  
+ATOM     13  C6    A A   1       0.298   8.207  -1.063  1.00  0.00           C  
+ATOM     14  N6    A A   1      -1.022   8.204  -1.236  1.00  0.00           N  
+ATOM     15  N1    A A   1       0.950   9.380  -0.971  1.00  0.00           N  
+ATOM     16  C2    A A   1       2.273   9.407  -0.803  1.00  0.00           C  
+ATOM     17  N3    A A   1       3.091   8.365  -0.708  1.00  0.00           N  
+ATOM     18  C4    A A   1       2.417   7.202  -0.802  1.00  0.00           C  
+ATOM     19 1H5*   A A   1       4.671   2.290  -2.305  1.00  0.00           H  
+ATOM     20 2H5*   A A   1       5.816   1.501  -1.189  1.00  0.00           H  
+ATOM     21  H4*   A A   1       6.646   3.694  -1.462  1.00  0.00           H  
+ATOM     22  H3*   A A   1       5.546   3.013   1.029  1.00  0.00           H  
+ATOM     23  H1*   A A   1       4.979   6.519  -0.638  1.00  0.00           H  
+ATOM     24  H8    A A   1       1.997   4.038  -0.875  1.00  0.00           H  
+ATOM     25 1H6    A A   1      -1.526   9.077  -1.294  1.00  0.00           H  
+ATOM     26 2H6    A A   1      -1.520   7.328  -1.309  1.00  0.00           H  
+ATOM     27  H2    A A   1       2.731  10.392  -0.730  1.00  0.00           H  
+ATOM     28 1H2*   A A   1       3.741   4.398   1.062  1.00  0.00           H  
+ATOM     29 2H2*   A A   1       4.989   5.649   1.459  1.00  0.00           H  
+ATOM     30  H5T   A A   1       3.298   1.508  -0.900  1.00  0.00           H  
+ATOM     31 P      T A   2       7.364   4.806   2.358  1.00  0.00           P  
+ATOM     32 O1P    T A   2       8.839   4.776   2.530  1.00  0.00           O  
+ATOM     33 O2P    T A   2       6.515   3.962   3.238  1.00  0.00           O  
+ATOM     34 O5*    T A   2       6.861   6.330   2.454  1.00  0.00           O  
+ATOM     35 C5*    T A   2       7.276   7.297   1.480  1.00  0.00           C  
+ATOM     36 C4*    T A   2       6.873   8.719   1.849  1.00  0.00           C  
+ATOM     37 O4*    T A   2       5.486   8.978   1.507  1.00  0.00           O  
+ATOM     38 C3*    T A   2       7.025   8.967   3.345  1.00  0.00           C  
+ATOM     39 O3*    T A   2       7.719  10.196   3.596  1.00  0.00           O  
+ATOM     40 C2*    T A   2       5.626   9.038   3.865  1.00  0.00           C  
+ATOM     41 C1*    T A   2       4.768   9.415   2.684  1.00  0.00           C  
+ATOM     42 N1     T A   2       3.423   8.799   2.747  1.00  0.00           N  
+ATOM     43 C2     T A   2       2.337   9.639   2.626  1.00  0.00           C  
+ATOM     44 O2     T A   2       2.458  10.860   2.552  1.00  0.00           O  
+ATOM     45 N3     T A   2       1.099   9.029   2.606  1.00  0.00           N  
+ATOM     46 C4     T A   2       0.851   7.673   2.697  1.00  0.00           C  
+ATOM     47 O4     T A   2      -0.302   7.243   2.661  1.00  0.00           O  
+ATOM     48 C5     T A   2       2.045   6.871   2.827  1.00  0.00           C  
+ATOM     49 C5M    T A   2       1.928   5.354   2.910  1.00  0.00           C  
+ATOM     50 C6     T A   2       3.266   7.442   2.852  1.00  0.00           C  
+ATOM     51 1H5*   T A   2       6.804   7.074   0.532  1.00  0.00           H  
+ATOM     52 2H5*   T A   2       8.368   7.233   1.371  1.00  0.00           H  
+ATOM     53 H4*    T A   2       7.506   9.419   1.306  1.00  0.00           H  
+ATOM     54 H3*    T A   2       7.553   8.132   3.808  1.00  0.00           H  
+ATOM     55 1H2*   T A   2       5.324   8.059   4.256  1.00  0.00           H  
+ATOM     56 2H2*   T A   2       5.564   9.815   4.630  1.00  0.00           H  
+ATOM     57 H1*    T A   2       4.665  10.500   2.653  1.00  0.00           H  
+ATOM     58 H3     T A   2       0.308   9.625   2.509  1.00  0.00           H  
+ATOM     59 1H5M   T A   2       1.213   5.085   3.678  1.00  0.00           H  
+ATOM     60 2H5M   T A   2       2.903   4.926   3.150  1.00  0.00           H  
+ATOM     61 3H5M   T A   2       1.589   4.964   1.960  1.00  0.00           H  
+ATOM     62 H6     T A   2       4.140   6.814   2.982  1.00  0.00           H  
+ATOM     63  P     C A   3       7.980  10.697   5.100  1.00  0.00           P  
+ATOM     64  O1P   C A   3       9.280  11.413   5.150  1.00  0.00           O  
+ATOM     65  O2P   C A   3       7.737   9.569   6.034  1.00  0.00           O  
+ATOM     66  O5*   C A   3       6.789  11.768   5.253  1.00  0.00           O  
+ATOM     67  C5*   C A   3       6.720  12.904   4.380  1.00  0.00           C  
+ATOM     68  C4*   C A   3       5.593  13.866   4.739  1.00  0.00           C  
+ATOM     69  O4*   C A   3       4.292  13.290   4.450  1.00  0.00           O  
+ATOM     70  C3*   C A   3       5.616  14.221   6.221  1.00  0.00           C  
+ATOM     71  O3*   C A   3       5.555  15.639   6.408  1.00  0.00           O  
+ATOM     72  C2*   C A   3       4.407  13.552   6.796  1.00  0.00           C  
+ATOM     73  C1*   C A   3       3.465  13.339   5.637  1.00  0.00           C  
+ATOM     74  N1    C A   3       2.672  12.098   5.790  1.00  0.00           N  
+ATOM     75  C2    C A   3       1.294  12.207   5.721  1.00  0.00           C  
+ATOM     76  O2    C A   3       0.763  13.308   5.588  1.00  0.00           O  
+ATOM     77  N3    C A   3       0.558  11.072   5.813  1.00  0.00           N  
+ATOM     78  C4    C A   3       1.140   9.878   5.968  1.00  0.00           C  
+ATOM     79  N4    C A   3       0.379   8.788   6.044  1.00  0.00           N  
+ATOM     80  C5    C A   3       2.559   9.760   6.045  1.00  0.00           C  
+ATOM     81  C6    C A   3       3.282  10.889   5.955  1.00  0.00           C  
+ATOM     82 1H5*   C A   3       6.534  12.568   3.369  1.00  0.00           H  
+ATOM     83 2H5*   C A   3       7.686  13.430   4.420  1.00  0.00           H  
+ATOM     84  H4*   C A   3       5.709  14.779   4.157  1.00  0.00           H  
+ATOM     85  H3*   C A   3       6.518  13.815   6.685  1.00  0.00           H  
+ATOM     86  H1*   C A   3       2.791  14.192   5.565  1.00  0.00           H  
+ATOM     87 1H4    C A   3       0.806   7.880   6.157  1.00  0.00           H  
+ATOM     88 2H4    C A   3      -0.626   8.869   5.991  1.00  0.00           H  
+ATOM     89  H5    C A   3       3.039   8.789   6.164  1.00  0.00           H  
+ATOM     90  H6    C A   3       4.365  10.840   6.032  1.00  0.00           H  
+ATOM     91 1H2*   C A   3       4.689  12.590   7.236  1.00  0.00           H  
+ATOM     92 2H2*   C A   3       3.940  14.214   7.534  1.00  0.00           H  
+ATOM     93  P     C A   4       5.538  16.275   7.882  1.00  0.00           P  
+ATOM     94  O1P   C A   4       6.177  17.615   7.835  1.00  0.00           O  
+ATOM     95  O2P   C A   4       6.033  15.266   8.851  1.00  0.00           O  
+ATOM     96  O5*   C A   4       3.955  16.462   8.083  1.00  0.00           O  
+ATOM     97  C5*   C A   4       3.157  17.011   7.025  1.00  0.00           C  
+ATOM     98  C4*   C A   4       1.722  17.289   7.449  1.00  0.00           C  
+ATOM     99  O4*   C A   4       0.888  16.113   7.280  1.00  0.00           O  
+ATOM    100  C3*   C A   4       1.648  17.697   8.914  1.00  0.00           C  
+ATOM    101  O3*   C A   4       0.881  18.892   9.085  1.00  0.00           O  
+ATOM    102  C2*   C A   4       0.992  16.545   9.602  1.00  0.00           C  
+ATOM    103  C1*   C A   4       0.232  15.803   8.531  1.00  0.00           C  
+ATOM    104  N1    C A   4       0.215  14.343   8.782  1.00  0.00           N  
+ATOM    105  C2    C A   4      -1.018  13.712   8.800  1.00  0.00           C  
+ATOM    106  O2    C A   4      -2.050  14.359   8.636  1.00  0.00           O  
+ATOM    107  N3    C A   4      -1.049  12.370   9.003  1.00  0.00           N  
+ATOM    108  C4    C A   4       0.078  11.668   9.183  1.00  0.00           C  
+ATOM    109  N4    C A   4       0.010  10.348   9.372  1.00  0.00           N  
+ATOM    110  C5    C A   4       1.351  12.313   9.169  1.00  0.00           C  
+ATOM    111  C6    C A   4       1.375  13.644   8.967  1.00  0.00           C  
+ATOM    112 1H5*   C A   4       3.112  16.305   6.208  1.00  0.00           H  
+ATOM    113 2H5*   C A   4       3.632  17.942   6.682  1.00  0.00           H  
+ATOM    114  H4*   C A   4       1.321  18.095   6.835  1.00  0.00           H  
+ATOM    115  H3*   C A   4       2.656  17.837   9.310  1.00  0.00           H  
+ATOM    116  H1*   C A   4      -0.791  16.175   8.498  1.00  0.00           H  
+ATOM    117 1H4    C A   4       0.855   9.814   9.502  1.00  0.00           H  
+ATOM    118 2H4    C A   4      -0.885   9.881   9.386  1.00  0.00           H  
+ATOM    119  H5    C A   4       2.272  11.748   9.314  1.00  0.00           H  
+ATOM    120  H6    C A   4       2.327  14.165   8.951  1.00  0.00           H  
+ATOM    121 1H2*   C A   4       1.751  15.896  10.049  1.00  0.00           H  
+ATOM    122 2H2*   C A   4       0.293  16.923  10.350  1.00  0.00           H  
+ATOM    123 P      T A   5       0.647  19.496  10.554  1.00  0.00           P  
+ATOM    124 O1P    T A   5       0.561  20.975  10.457  1.00  0.00           O  
+ATOM    125 O2P    T A   5       1.626  18.884  11.487  1.00  0.00           O  
+ATOM    126 O5*    T A   5      -0.815  18.907  10.868  1.00  0.00           O  
+ATOM    127 C5*    T A   5      -1.928  19.273  10.041  1.00  0.00           C  
+ATOM    128 C4*    T A   5      -3.200  18.507  10.381  1.00  0.00           C  
+ATOM    129 O4*    T A   5      -2.989  17.071  10.326  1.00  0.00           O  
+ATOM    130 C3*    T A   5      -3.691  18.844  11.781  1.00  0.00           C  
+ATOM    131 O3*    T A   5      -5.077  19.199  11.761  1.00  0.00           O  
+ATOM    132 C2*    T A   5      -3.465  17.594  12.579  1.00  0.00           C  
+ATOM    133 C1*    T A   5      -3.410  16.473  11.574  1.00  0.00           C  
+ATOM    134 N1     T A   5      -2.482  15.396  11.992  1.00  0.00           N  
+ATOM    135 C2     T A   5      -3.000  14.117  12.096  1.00  0.00           C  
+ATOM    136 O2     T A   5      -4.196  13.881  11.943  1.00  0.00           O  
+ATOM    137 N3     T A   5      -2.094  13.117  12.403  1.00  0.00           N  
+ATOM    138 C4     T A   5      -0.742  13.280  12.614  1.00  0.00           C  
+ATOM    139 O4     T A   5      -0.032  12.308  12.873  1.00  0.00           O  
+ATOM    140 C5     T A   5      -0.289  14.648  12.492  1.00  0.00           C  
+ATOM    141 C5M    T A   5       1.191  14.967  12.669  1.00  0.00           C  
+ATOM    142 C6     T A   5      -1.153  15.644  12.196  1.00  0.00           C  
+ATOM    143 1H5*   T A   5      -1.694  19.051   9.009  1.00  0.00           H  
+ATOM    144 2H5*   T A   5      -2.101  20.352  10.155  1.00  0.00           H  
+ATOM    145 H4*    T A   5      -3.974  18.774   9.662  1.00  0.00           H  
+ATOM    146 H3*    T A   5      -3.096  19.660  12.197  1.00  0.00           H  
+ATOM    147 1H2*   T A   5      -2.511  17.661  13.116  1.00  0.00           H  
+ATOM    148 2H2*   T A   5      -4.306  17.435  13.264  1.00  0.00           H  
+ATOM    149 H1*    T A   5      -4.409  16.057  11.449  1.00  0.00           H  
+ATOM    150 H3     T A   5      -2.449  12.182  12.472  1.00  0.00           H  
+ATOM    151 1H5M   T A   5       1.550  14.530  13.594  1.00  0.00           H  
+ATOM    152 2H5M   T A   5       1.333  16.047  12.693  1.00  0.00           H  
+ATOM    153 3H5M   T A   5       1.751  14.549  11.843  1.00  0.00           H  
+ATOM    154 H6     T A   5      -0.790  16.668  12.147  1.00  0.00           H  
+ATOM    155  P     A A   6      -5.692  20.169  12.882  1.00  0.00           P  
+ATOM    156  O1P   A A   6      -6.683  21.072  12.244  1.00  0.00           O  
+ATOM    157  O2P   A A   6      -4.583  20.752  13.678  1.00  0.00           O  
+ATOM    158  O5*   A A   6      -6.471  19.094  13.785  1.00  0.00           O  
+ATOM    159  C5*   A A   6      -7.541  18.319  13.232  1.00  0.00           C  
+ATOM    160  C4*   A A   6      -7.985  17.203  14.162  1.00  0.00           C  
+ATOM    161  O4*   A A   6      -7.060  16.084  14.109  1.00  0.00           O  
+ATOM    162  C3*   A A   6      -8.041  17.687  15.608  1.00  0.00           C  
+ATOM    163  O3*   A A   6      -9.285  17.318  16.221  1.00  0.00           O  
+ATOM    164  C2*   A A   6      -6.890  17.001  16.274  1.00  0.00           C  
+ATOM    165  C1*   A A   6      -6.626  15.770  15.448  1.00  0.00           C  
+ATOM    166  N9    A A   6      -5.206  15.361  15.499  1.00  0.00           N  
+ATOM    167  C8    A A   6      -4.070  16.107  15.522  1.00  0.00           C  
+ATOM    168  N7    A A   6      -2.949  15.480  15.662  1.00  0.00           N  
+ATOM    169  C5    A A   6      -3.380  14.152  15.741  1.00  0.00           C  
+ATOM    170  C6    A A   6      -2.701  12.939  15.900  1.00  0.00           C  
+ATOM    171  N6    A A   6      -1.379  12.855  16.045  1.00  0.00           N  
+ATOM    172  N1    A A   6      -3.441  11.818  15.931  1.00  0.00           N  
+ATOM    173  C2    A A   6      -4.769  11.882  15.816  1.00  0.00           C  
+ATOM    174  N3    A A   6      -5.509  12.969  15.668  1.00  0.00           N  
+ATOM    175  C4    A A   6      -4.749  14.077  15.638  1.00  0.00           C  
+ATOM    176 1H5*   A A   6      -7.211  17.850  12.315  1.00  0.00           H  
+ATOM    177 2H5*   A A   6      -8.386  18.991  13.021  1.00  0.00           H  
+ATOM    178  H4*   A A   6      -8.974  16.858  13.863  1.00  0.00           H  
+ATOM    179  H3*   A A   6      -7.903  18.770  15.646  1.00  0.00           H  
+ATOM    180  H1*   A A   6      -7.241  14.954  15.831  1.00  0.00           H  
+ATOM    181  H8    A A   6      -4.100  17.190  15.422  1.00  0.00           H  
+ATOM    182 1H6    A A   6      -0.941  11.951  16.157  1.00  0.00           H  
+ATOM    183 2H6    A A   6      -0.816  13.693  16.045  1.00  0.00           H  
+ATOM    184  H2    A A   6      -5.306  10.937  15.837  1.00  0.00           H  
+ATOM    185 1H2*   A A   6      -6.014  17.659  16.261  1.00  0.00           H  
+ATOM    186 2H2*   A A   6      -7.162  16.715  17.291  1.00  0.00           H  
+ATOM    187  P     G A   7      -9.843  18.105  17.507  1.00  0.00           P  
+ATOM    188  O1P   G A   7     -11.229  18.561  17.226  1.00  0.00           O  
+ATOM    189  O2P   G A   7      -8.828  19.100  17.939  1.00  0.00           O  
+ATOM    190  O5*   G A   7      -9.897  16.910  18.585  1.00  0.00           O  
+ATOM    191  C5*   G A   7     -10.177  15.560  18.181  1.00  0.00           C  
+ATOM    192  C4*   G A   7      -9.561  14.522  19.125  1.00  0.00           C  
+ATOM    193  O4*   G A   7      -8.133  14.405  18.887  1.00  0.00           O  
+ATOM    194  C3*   G A   7      -9.744  14.878  20.608  1.00  0.00           C  
+ATOM    195  O3*   G A   7     -10.214  13.747  21.352  1.00  0.00           O  
+ATOM    196  C2*   G A   7      -8.383  15.282  21.074  1.00  0.00           C  
+ATOM    197  C1*   G A   7      -7.410  14.638  20.119  1.00  0.00           C  
+ATOM    198  N9    G A   7      -6.233  15.500  19.896  1.00  0.00           N  
+ATOM    199  C8    G A   7      -6.168  16.829  19.630  1.00  0.00           C  
+ATOM    200  N7    G A   7      -4.998  17.354  19.481  1.00  0.00           N  
+ATOM    201  C5    G A   7      -4.162  16.248  19.668  1.00  0.00           C  
+ATOM    202  C6    G A   7      -2.744  16.163  19.632  1.00  0.00           C  
+ATOM    203  O6    G A   7      -1.932  17.060  19.420  1.00  0.00           O  
+ATOM    204  N1    G A   7      -2.305  14.867  19.874  1.00  0.00           N  
+ATOM    205  C2    G A   7      -3.123  13.783  20.119  1.00  0.00           C  
+ATOM    206  N2    G A   7      -2.510  12.617  20.326  1.00  0.00           N  
+ATOM    207  N3    G A   7      -4.458  13.854  20.155  1.00  0.00           N  
+ATOM    208  C4    G A   7      -4.911  15.108  19.923  1.00  0.00           C  
+ATOM    209 1H5*   G A   7      -9.745  15.381  17.207  1.00  0.00           H  
+ATOM    210 2H5*   G A   7     -11.270  15.426  18.114  1.00  0.00           H  
+ATOM    211  H4*   G A   7     -10.025  13.556  18.935  1.00  0.00           H  
+ATOM    212  H3*   G A   7     -10.429  15.719  20.727  1.00  0.00           H  
+ATOM    213  H1*   G A   7      -7.083  13.684  20.529  1.00  0.00           H  
+ATOM    214  H8    G A   7      -7.071  17.433  19.552  1.00  0.00           H  
+ATOM    215  H1    G A   7      -1.305  14.730  19.867  1.00  0.00           H  
+ATOM    216 1H2    G A   7      -1.501  12.565  20.299  1.00  0.00           H  
+ATOM    217 2H2    G A   7      -3.053  11.785  20.505  1.00  0.00           H  
+ATOM    218 1H2*   G A   7      -8.286  16.373  21.035  1.00  0.00           H  
+ATOM    219 2H2*   G A   7      -8.214  14.899  22.086  1.00  0.00           H  
+ATOM    220 P      T A   8     -10.470  13.861  22.933  1.00  0.00           P  
+ATOM    221 O1P    T A   8     -11.662  13.049  23.287  1.00  0.00           O  
+ATOM    222 O2P    T A   8     -10.423  15.292  23.326  1.00  0.00           O  
+ATOM    223 O5*    T A   8      -9.152  13.125  23.489  1.00  0.00           O  
+ATOM    224 C5*    T A   8      -9.105  11.695  23.588  1.00  0.00           C  
+ATOM    225 C4*    T A   8      -7.687  11.168  23.791  1.00  0.00           C  
+ATOM    226 O4*    T A   8      -6.715  12.044  23.168  1.00  0.00           O  
+ATOM    227 C3*    T A   8      -7.326  11.065  25.272  1.00  0.00           C  
+ATOM    228 O3*    T A   8      -6.760   9.782  25.572  1.00  0.00           O  
+ATOM    229 C2*    T A   8      -6.324  12.155  25.493  1.00  0.00           C  
+ATOM    230 C1*    T A   8      -5.719  12.435  24.137  1.00  0.00           C  
+ATOM    231 N1     T A   8      -5.347  13.860  23.988  1.00  0.00           N  
+ATOM    232 C2     T A   8      -4.038  14.136  23.637  1.00  0.00           C  
+ATOM    233 O2     T A   8      -3.212  13.247  23.443  1.00  0.00           O  
+ATOM    234 N3     T A   8      -3.711  15.473  23.513  1.00  0.00           N  
+ATOM    235 C4     T A   8      -4.564  16.543  23.707  1.00  0.00           C  
+ATOM    236 O4     T A   8      -4.163  17.697  23.570  1.00  0.00           O  
+ATOM    237 C5     T A   8      -5.910  16.163  24.071  1.00  0.00           C  
+ATOM    238 C5M    T A   8      -6.952  17.250  24.322  1.00  0.00           C  
+ATOM    239 C6     T A   8      -6.259  14.865  24.197  1.00  0.00           C  
+ATOM    240 1H5*   T A   8      -9.468  11.262  22.666  1.00  0.00           H  
+ATOM    241 2H5*   T A   8      -9.754  11.381  24.418  1.00  0.00           H  
+ATOM    242 H4*    T A   8      -7.609  10.181  23.338  1.00  0.00           H  
+ATOM    243 H3*    T A   8      -8.207  11.245  25.890  1.00  0.00           H  
+ATOM    244 1H2*   T A   8      -6.834  13.050  25.864  1.00  0.00           H  
+ATOM    245 2H2*   T A   8      -5.551  11.817  26.188  1.00  0.00           H  
+ATOM    246 H1*    T A   8      -4.826  11.809  24.000  1.00  0.00           H  
+ATOM    247 H3     T A   8      -2.758  15.688  23.257  1.00  0.00           H  
+ATOM    248 1H5M   T A   8      -7.951  16.823  24.241  1.00  0.00           H  
+ATOM    249 2H5M   T A   8      -6.834  18.044  23.584  1.00  0.00           H  
+ATOM    250 3H5M   T A   8      -6.813  17.662  25.322  1.00  0.00           H  
+ATOM    251 H6     T A   8      -7.285  14.614  24.463  1.00  0.00           H  
+ATOM    252 P      T A   9      -6.511   9.330  27.094  1.00  0.00           P  
+ATOM    253 O1P    T A   9      -6.391   7.851  27.145  1.00  0.00           O  
+ATOM    254 O2P    T A   9      -7.505  10.007  27.965  1.00  0.00           O  
+ATOM    255 O5*    T A   9      -5.064   9.980  27.352  1.00  0.00           O  
+ATOM    256 C5*    T A   9      -3.880   9.385  26.799  1.00  0.00           C  
+ATOM    257 C4*    T A   9      -3.160  10.317  25.831  1.00  0.00           C  
+ATOM    258 O4*    T A   9      -3.322  11.705  26.223  1.00  0.00           O  
+ATOM    259 C3*    T A   9      -1.667  10.028  25.792  1.00  0.00           C  
+ATOM    260 O3*    T A   9      -1.201   9.937  24.447  1.00  0.00           O  
+ATOM    261 C2*    T A   9      -1.031  11.183  26.492  1.00  0.00           C  
+ATOM    262 C1*    T A   9      -2.022  12.314  26.402  1.00  0.00           C  
+ATOM    263 N1     T A   9      -1.980  13.144  27.620  1.00  0.00           N  
+ATOM    264 C2     T A   9      -1.594  14.462  27.479  1.00  0.00           C  
+ATOM    265 O2     T A   9      -1.304  14.946  26.388  1.00  0.00           O  
+ATOM    266 N3     T A   9      -1.550  15.208  28.642  1.00  0.00           N  
+ATOM    267 C4     T A   9      -1.856  14.754  29.913  1.00  0.00           C  
+ATOM    268 O4     T A   9      -1.781  15.506  30.882  1.00  0.00           O  
+ATOM    269 C5     T A   9      -2.250  13.364  29.961  1.00  0.00           C  
+ATOM    270 C5M    T A   9      -2.613  12.733  31.301  1.00  0.00           C  
+ATOM    271 C6     T A   9      -2.301  12.617  28.841  1.00  0.00           C  
+ATOM    272 1H5*   T A   9      -4.151   8.500  26.239  1.00  0.00           H  
+ATOM    273 2H5*   T A   9      -3.212   9.106  27.628  1.00  0.00           H  
+ATOM    274 H4*    T A   9      -3.569  10.180  24.831  1.00  0.00           H  
+ATOM    275 H3*    T A   9      -1.452   9.104  26.331  1.00  0.00           H  
+ATOM    276 1H2*   T A   9      -0.850  10.929  27.544  1.00  0.00           H  
+ATOM    277 2H2*   T A   9      -0.104  11.461  25.976  1.00  0.00           H  
+ATOM    278 H1*    T A   9      -1.789  12.931  25.535  1.00  0.00           H  
+ATOM    279 H3     T A   9      -1.266  16.173  28.556  1.00  0.00           H  
+ATOM    280 1H5M   T A   9      -3.440  13.282  31.750  1.00  0.00           H  
+ATOM    281 2H5M   T A   9      -1.749  12.768  31.965  1.00  0.00           H  
+ATOM    282 3H5M   T A   9      -2.907  11.695  31.144  1.00  0.00           H  
+ATOM    283 H6     T A   9      -2.602  11.572  28.910  1.00  0.00           H  
+ATOM    284  P     A A  10      -0.315   8.688  23.992  1.00  0.00           P  
+ATOM    285  O1P   A A  10       0.551   8.277  25.125  1.00  0.00           O  
+ATOM    286  O2P   A A  10       0.304   8.985  22.676  1.00  0.00           O  
+ATOM    287  O5*   A A  10      -1.467   7.588  23.799  1.00  0.00           O  
+ATOM    288  C5*   A A  10      -1.147   6.209  23.981  1.00  0.00           C  
+ATOM    289  C4*   A A  10      -1.836   5.303  22.968  1.00  0.00           C  
+ATOM    290  O4*   A A  10      -3.058   5.912  22.482  1.00  0.00           O  
+ATOM    291  C3*   A A  10      -0.922   5.089  21.772  1.00  0.00           C  
+ATOM    292  O3*   A A  10      -1.116   3.794  21.200  1.00  0.00           O  
+ATOM    293  C2*   A A  10      -1.353   6.163  20.832  1.00  0.00           C  
+ATOM    294  C1*   A A  10      -2.814   6.401  21.156  1.00  0.00           C  
+ATOM    295  N9    A A  10      -3.245   7.804  21.056  1.00  0.00           N  
+ATOM    296  C8    A A  10      -2.525   8.939  21.164  1.00  0.00           C  
+ATOM    297  N7    A A  10      -3.166  10.059  21.189  1.00  0.00           N  
+ATOM    298  C5    A A  10      -4.488   9.625  21.105  1.00  0.00           C  
+ATOM    299  C6    A A  10      -5.708  10.306  21.082  1.00  0.00           C  
+ATOM    300  N6    A A  10      -5.798  11.634  21.109  1.00  0.00           N  
+ATOM    301  N1    A A  10      -6.829   9.568  20.995  1.00  0.00           N  
+ATOM    302  C2    A A  10      -6.756   8.238  20.930  1.00  0.00           C  
+ATOM    303  N3    A A  10      -5.655   7.493  20.942  1.00  0.00           N  
+ATOM    304  C4    A A  10      -4.547   8.257  21.031  1.00  0.00           C  
+ATOM    305 1H5*   A A  10      -1.499   5.914  24.943  1.00  0.00           H  
+ATOM    306 2H5*   A A  10      -0.058   6.091  23.938  1.00  0.00           H  
+ATOM    307  H4*   A A  10      -2.067   4.345  23.431  1.00  0.00           H  
+ATOM    308  H3*   A A  10       0.123   5.233  22.050  1.00  0.00           H  
+ATOM    309  H1*   A A  10      -3.405   5.820  20.462  1.00  0.00           H  
+ATOM    310  H8    A A  10      -1.467   8.901  21.352  1.00  0.00           H  
+ATOM    311 1H6    A A  10      -4.961  12.197  21.148  1.00  0.00           H  
+ATOM    312 2H6    A A  10      -6.705  12.077  21.097  1.00  0.00           H  
+ATOM    313  H2    A A  10      -7.703   7.703  20.862  1.00  0.00           H  
+ATOM    314 1H2*   A A  10      -0.763   7.061  21.013  1.00  0.00           H  
+ATOM    315 2H2*   A A  10      -1.255   5.812  19.797  1.00  0.00           H  
+ATOM    316 P      T A  11      -0.300   3.354  19.891  1.00  0.00           P  
+ATOM    317 O1P    T A  11       0.097   1.930  20.024  1.00  0.00           O  
+ATOM    318 O2P    T A  11       0.734   4.378  19.599  1.00  0.00           O  
+ATOM    319 O5*    T A  11      -1.473   3.469  18.803  1.00  0.00           O  
+ATOM    320 C5*    T A  11      -2.662   2.689  18.966  1.00  0.00           C  
+ATOM    321 C4*    T A  11      -3.851   3.245  18.197  1.00  0.00           C  
+ATOM    322 O4*    T A  11      -3.901   4.696  18.258  1.00  0.00           O  
+ATOM    323 C3*    T A  11      -3.793   2.852  16.729  1.00  0.00           C  
+ATOM    324 O3*    T A  11      -5.015   2.233  16.322  1.00  0.00           O  
+ATOM    325 C2*    T A  11      -3.564   4.136  15.992  1.00  0.00           C  
+ATOM    326 C1*    T A  11      -4.030   5.228  16.919  1.00  0.00           C  
+ATOM    327 N1     T A  11      -3.239   6.466  16.744  1.00  0.00           N  
+ATOM    328 C2     T A  11      -3.928   7.616  16.410  1.00  0.00           C  
+ATOM    329 O2     T A  11      -5.147   7.627  16.255  1.00  0.00           O  
+ATOM    330 N3     T A  11      -3.167   8.760  16.267  1.00  0.00           N  
+ATOM    331 C4     T A  11      -1.796   8.854  16.430  1.00  0.00           C  
+ATOM    332 O4     T A  11      -1.220   9.932  16.292  1.00  0.00           O  
+ATOM    333 C5     T A  11      -1.161   7.602  16.776  1.00  0.00           C  
+ATOM    334 C5M    T A  11       0.348   7.560  16.990  1.00  0.00           C  
+ATOM    335 C6     T A  11      -1.881   6.470  16.918  1.00  0.00           C  
+ATOM    336 1H5*   T A  11      -2.944   2.680  20.010  1.00  0.00           H  
+ATOM    337 2H5*   T A  11      -2.451   1.662  18.634  1.00  0.00           H  
+ATOM    338 H4*    T A  11      -4.766   2.847  18.632  1.00  0.00           H  
+ATOM    339 H3*    T A  11      -2.953   2.176  16.559  1.00  0.00           H  
+ATOM    340 1H2*   T A  11      -2.495   4.258  15.779  1.00  0.00           H  
+ATOM    341 2H2*   T A  11      -4.165   4.148  15.075  1.00  0.00           H  
+ATOM    342 H1*    T A  11      -5.080   5.439  16.719  1.00  0.00           H  
+ATOM    343 H3     T A  11      -3.656   9.597  16.002  1.00  0.00           H  
+ATOM    344 1H5M   T A  11       0.804   8.445  16.550  1.00  0.00           H  
+ATOM    345 2H5M   T A  11       0.757   6.667  16.526  1.00  0.00           H  
+ATOM    346 3H5M   T A  11       0.561   7.538  18.049  1.00  0.00           H  
+ATOM    347 H6     T A  11      -1.372   5.540  17.168  1.00  0.00           H  
+ATOM    348  P     A A  12      -5.221   1.752  14.807  1.00  0.00           P  
+ATOM    349  O1P   A A  12      -6.125   0.574  14.792  1.00  0.00           O  
+ATOM    350  O2P   A A  12      -3.895   1.663  14.146  1.00  0.00           O  
+ATOM    351  O5*   A A  12      -6.010   3.023  14.225  1.00  0.00           O  
+ATOM    352  C5*   A A  12      -7.077   3.615  14.980  1.00  0.00           C  
+ATOM    353  C4*   A A  12      -7.824   4.680  14.194  1.00  0.00           C  
+ATOM    354  O4*   A A  12      -7.144   5.958  14.280  1.00  0.00           O  
+ATOM    355  C3*   A A  12      -7.909   4.308  12.721  1.00  0.00           C  
+ATOM    356  O3*   A A  12      -9.231   4.514  12.212  1.00  0.00           O  
+ATOM    357  C2*   A A  12      -6.935   5.215  12.045  1.00  0.00           C  
+ATOM    358  C1*   A A  12      -6.790   6.408  12.952  1.00  0.00           C  
+ATOM    359  N9    A A  12      -5.417   6.949  12.917  1.00  0.00           N  
+ATOM    360  C8    A A  12      -4.226   6.316  13.057  1.00  0.00           C  
+ATOM    361  N7    A A  12      -3.157   7.043  13.020  1.00  0.00           N  
+ATOM    362  C5    A A  12      -3.693   8.321  12.830  1.00  0.00           C  
+ATOM    363  C6    A A  12      -3.111   9.589  12.699  1.00  0.00           C  
+ATOM    364  N6    A A  12      -1.795   9.805  12.753  1.00  0.00           N  
+ATOM    365  N1    A A  12      -3.941  10.629  12.522  1.00  0.00           N  
+ATOM    366  C2    A A  12      -5.257  10.448  12.476  1.00  0.00           C  
+ATOM    367  N3    A A  12      -5.913   9.300  12.587  1.00  0.00           N  
+ATOM    368  C4    A A  12      -5.067   8.268  12.764  1.00  0.00           C  
+ATOM    369 1H5*   A A  12      -6.670   4.100  15.857  1.00  0.00           H  
+ATOM    370 2H5*   A A  12      -7.769   2.818  15.287  1.00  0.00           H  
+ATOM    371  H4*   A A  12      -8.830   4.786  14.598  1.00  0.00           H  
+ATOM    372  H3*   A A  12      -7.606   3.268  12.582  1.00  0.00           H  
+ATOM    373  H1*   A A  12      -7.490   7.183  12.639  1.00  0.00           H  
+ATOM    374  H8    A A  12      -4.171   5.237  13.186  1.00  0.00           H  
+ATOM    375 1H6    A A  12      -1.162   9.032  12.894  1.00  0.00           H  
+ATOM    376 2H6    A A  12      -1.429  10.745  12.648  1.00  0.00           H  
+ATOM    377  H2    A A  12      -5.861  11.340  12.337  1.00  0.00           H  
+ATOM    378 1H2*   A A  12      -5.967   4.711  11.933  1.00  0.00           H  
+ATOM    379 2H2*   A A  12      -7.341   5.533  11.081  1.00  0.00           H  
+ATOM    380  P     G A  13      -9.569   4.219  10.669  1.00  0.00           P  
+ATOM    381  O1P   G A  13     -10.964   3.722  10.568  1.00  0.00           O  
+ATOM    382  O2P   G A  13      -8.467   3.416  10.078  1.00  0.00           O  
+ATOM    383  O5*   G A  13      -9.502   5.712  10.074  1.00  0.00           O  
+ATOM    384  C5*   G A  13     -10.262   6.771  10.674  1.00  0.00           C  
+ATOM    385  C4*   G A  13     -10.106   8.098   9.939  1.00  0.00           C  
+ATOM    386  O4*   G A  13      -8.786   8.662  10.158  1.00  0.00           O  
+ATOM    387  C3*   G A  13     -10.275   7.918   8.438  1.00  0.00           C  
+ATOM    388  O3*   G A  13     -11.101   8.949   7.886  1.00  0.00           O  
+ATOM    389  C2*   G A  13      -8.891   8.009   7.886  1.00  0.00           C  
+ATOM    390  C1*   G A  13      -8.107   8.815   8.888  1.00  0.00           C  
+ATOM    391  N9    G A  13      -6.709   8.354   8.973  1.00  0.00           N  
+ATOM    392  C8    G A  13      -6.219   7.099   9.112  1.00  0.00           C  
+ATOM    393  N7    G A  13      -4.941   6.963   9.220  1.00  0.00           N  
+ATOM    394  C5    G A  13      -4.509   8.289   9.140  1.00  0.00           C  
+ATOM    395  C6    G A  13      -3.197   8.821   9.193  1.00  0.00           C  
+ATOM    396  O6    G A  13      -2.131   8.221   9.329  1.00  0.00           O  
+ATOM    397  N1    G A  13      -3.206  10.202   9.073  1.00  0.00           N  
+ATOM    398  C2    G A  13      -4.330  10.984   8.915  1.00  0.00           C  
+ATOM    399  N2    G A  13      -4.124  12.296   8.784  1.00  0.00           N  
+ATOM    400  N3    G A  13      -5.570  10.492   8.868  1.00  0.00           N  
+ATOM    401  C4    G A  13      -5.588   9.146   8.985  1.00  0.00           C  
+ATOM    402 1H5*   G A  13      -9.915   6.931  11.687  1.00  0.00           H  
+ATOM    403 2H5*   G A  13     -11.321   6.472  10.690  1.00  0.00           H  
+ATOM    404  H4*   G A  13     -10.856   8.800  10.304  1.00  0.00           H  
+ATOM    405  H3*   G A  13     -10.699   6.935   8.226  1.00  0.00           H  
+ATOM    406  H1*   G A  13      -8.123   9.865   8.595  1.00  0.00           H  
+ATOM    407  H8    G A  13      -6.878   6.234   9.115  1.00  0.00           H  
+ATOM    408  H1    G A  13      -2.315  10.646   9.124  1.00  0.00           H  
+ATOM    409 1H2    G A  13      -3.184  12.667   8.819  1.00  0.00           H  
+ATOM    410 2H2    G A  13      -4.906  12.918   8.649  1.00  0.00           H  
+ATOM    411 1H2*   G A  13      -8.460   7.004   7.796  1.00  0.00           H  
+ATOM    412 2H2*   G A  13      -8.913   8.529   6.925  1.00  0.00           H  
+ATOM    413  P     G A  14     -11.390   9.003   6.307  1.00  0.00           P  
+ATOM    414  O1P   G A  14     -12.822   9.326   6.088  1.00  0.00           O  
+ATOM    415  O2P   G A  14     -10.812   7.792   5.669  1.00  0.00           O  
+ATOM    416  O5*   G A  14     -10.498  10.281   5.903  1.00  0.00           O  
+ATOM    417  C5*   G A  14     -10.655  11.527   6.598  1.00  0.00           C  
+ATOM    418  C4*   G A  14      -9.695  12.606   6.108  1.00  0.00           C  
+ATOM    419  O4*   G A  14      -8.331  12.331   6.524  1.00  0.00           O  
+ATOM    420  C3*   G A  14      -9.699  12.699   4.588  1.00  0.00           C  
+ATOM    421  O3*   G A  14      -9.858  14.054   4.155  1.00  0.00           O  
+ATOM    422  C2*   G A  14      -8.370  12.156   4.168  1.00  0.00           C  
+ATOM    423  C1*   G A  14      -7.466  12.306   5.364  1.00  0.00           C  
+ATOM    424  N9    G A  14      -6.496  11.197   5.439  1.00  0.00           N  
+ATOM    425  C8    G A  14      -6.712   9.862   5.468  1.00  0.00           C  
+ATOM    426  N7    G A  14      -5.685   9.089   5.544  1.00  0.00           N  
+ATOM    427  C5    G A  14      -4.640  10.014   5.568  1.00  0.00           C  
+ATOM    428  C6    G A  14      -3.243   9.800   5.643  1.00  0.00           C  
+ATOM    429  O6    G A  14      -2.637   8.733   5.710  1.00  0.00           O  
+ATOM    430  N1    G A  14      -2.546  11.000   5.639  1.00  0.00           N  
+ATOM    431  C2    G A  14      -3.115  12.253   5.569  1.00  0.00           C  
+ATOM    432  N2    G A  14      -2.272  13.284   5.569  1.00  0.00           N  
+ATOM    433  N3    G A  14      -4.431  12.464   5.499  1.00  0.00           N  
+ATOM    434  C4    G A  14      -5.130  11.309   5.503  1.00  0.00           C  
+ATOM    435 1H5*   G A  14     -10.451  11.380   7.649  1.00  0.00           H  
+ATOM    436 2H5*   G A  14     -11.694  11.866   6.469  1.00  0.00           H  
+ATOM    437  H4*   G A  14     -10.002  13.566   6.522  1.00  0.00           H  
+ATOM    438  H3*   G A  14     -10.498  12.075   4.180  1.00  0.00           H  
+ATOM    439  H1*   G A  14      -6.929  13.252   5.293  1.00  0.00           H  
+ATOM    440  H8    G A  14      -7.718   9.456   5.407  1.00  0.00           H  
+ATOM    441  H1    G A  14      -1.553  10.927   5.697  1.00  0.00           H  
+ATOM    442 1H2    G A  14      -1.276  13.122   5.619  1.00  0.00           H  
+ATOM    443 2H2    G A  14      -2.629  14.227   5.521  1.00  0.00           H  
+ATOM    444 1H2*   G A  14      -8.468  11.095   3.906  1.00  0.00           H  
+ATOM    445 2H2*   G A  14      -7.981  12.746   3.333  1.00  0.00           H  
+ATOM    446  P     A A  15      -9.872  14.418   2.591  1.00  0.00           P  
+ATOM    447  O1P   A A  15     -10.717  15.621   2.385  1.00  0.00           O  
+ATOM    448  O2P   A A  15     -10.159  13.187   1.811  1.00  0.00           O  
+ATOM    449  O5*   A A  15      -8.329  14.822   2.384  1.00  0.00           O  
+ATOM    450  C5*   A A  15      -7.757  15.905   3.132  1.00  0.00           C  
+ATOM    451  C4*   A A  15      -6.352  16.267   2.666  1.00  0.00           C  
+ATOM    452  O4*   A A  15      -5.384  15.271   3.088  1.00  0.00           O  
+ATOM    453  C3*   A A  15      -6.283  16.352   1.147  1.00  0.00           C  
+ATOM    454  O3*   A A  15      -5.624  17.548   0.722  1.00  0.00           O  
+ATOM    455  C2*   A A  15      -5.504  15.149   0.731  1.00  0.00           C  
+ATOM    456  C1*   A A  15      -4.683  14.758   1.931  1.00  0.00           C  
+ATOM    457  N9    A A  15      -4.519  13.297   2.002  1.00  0.00           N  
+ATOM    458  C8    A A  15      -5.449  12.315   1.922  1.00  0.00           C  
+ATOM    459  N7    A A  15      -5.037  11.096   2.004  1.00  0.00           N  
+ATOM    460  C5    A A  15      -3.661  11.277   2.155  1.00  0.00           C  
+ATOM    461  C6    A A  15      -2.600  10.384   2.299  1.00  0.00           C  
+ATOM    462  N6    A A  15      -2.755   9.059   2.312  1.00  0.00           N  
+ATOM    463  N1    A A  15      -1.372  10.906   2.425  1.00  0.00           N  
+ATOM    464  C2    A A  15      -1.189  12.224   2.412  1.00  0.00           C  
+ATOM    465  N3    A A  15      -2.117  13.160   2.280  1.00  0.00           N  
+ATOM    466  C4    A A  15      -3.341  12.615   2.156  1.00  0.00           C  
+ATOM    467 1H5*   A A  15      -7.679  15.620   4.173  1.00  0.00           H  
+ATOM    468 2H5*   A A  15      -8.419  16.778   3.038  1.00  0.00           H  
+ATOM    469  H4*   A A  15      -6.074  17.231   3.090  1.00  0.00           H  
+ATOM    470  H3*   A A  15      -7.289  16.303   0.726  1.00  0.00           H  
+ATOM    471  H1*   A A  15      -3.701  15.229   1.864  1.00  0.00           H  
+ATOM    472  H8    A A  15      -6.501  12.547   1.781  1.00  0.00           H  
+ATOM    473 1H6    A A  15      -1.949   8.456   2.417  1.00  0.00           H  
+ATOM    474 2H6    A A  15      -3.677   8.658   2.219  1.00  0.00           H  
+ATOM    475  H2    A A  15      -0.165  12.572   2.528  1.00  0.00           H  
+ATOM    476 1H2*   A A  15      -6.190  14.335   0.468  1.00  0.00           H  
+ATOM    477 2H2*   A A  15      -4.844  15.409  -0.102  1.00  0.00           H  
+ATOM    478 P      T A  16      -5.398  17.836  -0.841  1.00  0.00           P  
+ATOM    479 O1P    T A  16      -5.436  19.302  -1.072  1.00  0.00           O  
+ATOM    480 O2P    T A  16      -6.293  16.951  -1.628  1.00  0.00           O  
+ATOM    481 O5*    T A  16      -3.882  17.322  -1.001  1.00  0.00           O  
+ATOM    482 C5*    T A  16      -2.838  17.907  -0.211  1.00  0.00           C  
+ATOM    483 C4*    T A  16      -1.452  17.388  -0.574  1.00  0.00           C  
+ATOM    484 O4*    T A  16      -1.281  16.003  -0.170  1.00  0.00           O  
+ATOM    485 C3*    T A  16      -1.207  17.463  -2.076  1.00  0.00           C  
+ATOM    486 O3*    T A  16       0.021  18.138  -2.365  1.00  0.00           O  
+ATOM    487 C2*    T A  16      -1.160  16.036  -2.531  1.00  0.00           C  
+ATOM    488 C1*    T A  16      -0.834  15.221  -1.300  1.00  0.00           C  
+ATOM    489 N1     T A  16      -1.493  13.897  -1.332  1.00  0.00           N  
+ATOM    490 C2     T A  16      -0.686  12.781  -1.194  1.00  0.00           C  
+ATOM    491 O2     T A  16       0.530  12.869  -1.037  1.00  0.00           O  
+ATOM    492 N3     T A  16      -1.328  11.558  -1.246  1.00  0.00           N  
+ATOM    493 C4     T A  16      -2.685  11.356  -1.424  1.00  0.00           C  
+ATOM    494 O4     T A  16      -3.150  10.219  -1.466  1.00  0.00           O  
+ATOM    495 C5     T A  16      -3.447  12.577  -1.557  1.00  0.00           C  
+ATOM    496 C5M    T A  16      -4.957  12.501  -1.760  1.00  0.00           C  
+ATOM    497 C6     T A  16      -2.847  13.782  -1.508  1.00  0.00           C  
+ATOM    498 1H5*   T A  16      -2.999  17.667   0.830  1.00  0.00           H  
+ATOM    499 2H5*   T A  16      -2.874  18.998  -0.347  1.00  0.00           H  
+ATOM    500 H4*    T A  16      -0.705  17.995  -0.065  1.00  0.00           H  
+ATOM    501 H3*    T A  16      -2.043  17.975  -2.561  1.00  0.00           H  
+ATOM    502 1H2*   T A  16      -2.137  15.741  -2.930  1.00  0.00           H  
+ATOM    503 2H2*   T A  16      -0.365  15.912  -3.277  1.00  0.00           H  
+ATOM    504 H1*    T A  16       0.246  15.085  -1.238  1.00  0.00           H  
+ATOM    505 H3     T A  16      -0.760  10.742  -1.134  1.00  0.00           H  
+ATOM    506 1H5M   T A  16      -5.422  13.407  -1.376  1.00  0.00           H  
+ATOM    507 2H5M   T A  16      -5.352  11.634  -1.237  1.00  0.00           H  
+ATOM    508 3H5M   T A  16      -5.176  12.408  -2.814  1.00  0.00           H  
+ATOM    509 H6     T A  16      -3.452  14.681  -1.599  1.00  0.00           H  
+ATOM    510 H3T    T A  16       0.690  17.465  -2.514  1.00  0.00           H  
+TER     511        T A  16                                                      
+ENDMDL                                                                          

tools/ch2lmp/example/1ac7_trj.psf

@@ -0,0 +1 @@
+1ac7_ctrl.psf

tools/ch2lmp/example/top_all27_na.rtf

@@ -0,0 +1,939 @@
+*  \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////
+*  \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
+*   Alexander D. MacKerell Jr. and Nicolas Foloppe
+*                     December, 2003
+* All comments to ADM jr. via the CHARMM web site: www.charmm.org
+*               parameter set discussion forum
+*
+27 1
+
+! model componds moved to toppar_all27_na_model.str
+
+! NAD, ATP, PPI and related compounds moved to toppar_all27_na_nad_ppi.str
+
+! base modification residues and patches moved to toppar_all27_na_base_modifications.str
+
+! 
+!references
+!
+!NUCLEIC ACIDS
+!
+!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
+!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
+!Condensed Phase Macromolecular Target Data. 2000, 21: 86-104.
+!
+!and
+!
+!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
+!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
+!and RNA in Solution. 2000, 21: 105-120.
+!
+
+MASS 1    HT    1.008000 H ! TIPS3P WATER HYDROGEN
+MASS 2    HN1   1.008000 H ! Nucleic acid amine proton
+MASS 3    HN2   1.008000 H ! Nucleic acid ring nitrogen proton
+MASS 4    HN3   1.008000 H ! Nucleic acid aromatic carbon proton
+MASS 5    HN3B  1.008000 H ! NAD+ aromatic hydrogen
+MASS 6    HN3C  1.008000 H ! Standard aromatic hydrogen (as in benzene)
+MASS 7    HNP   1.008000 H ! pure aromatic H
+MASS 8    HN4   1.008000 H ! Nucleic acid phosphate hydroxyl proton
+MASS 9    HN5   1.008000 H ! Nucleic acid ribose hydroxyl proton
+MASS 10   HN6   1.008000 H ! Nucleic acid ribose aliphatic proton
+MASS 11   HN7   1.008000 H ! Nucleic acid proton (equivalent to protein HA)
+MASS 12   HN8   1.008000 H ! Bound to CN8 in nucleic acids/model compounds
+MASS 13   HN9   1.008000 H ! Bound to CN9 in nucleic acids/model compounds
+MASS 14   HNE1  1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha)
+MASS 15   HNE2  1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha)
+MASS 20   CN1  12.011000 C ! Nucleic acid carbonyl carbon
+MASS 21   CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon
+MASS 22   CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2)
+MASS 23   CN2  12.011000 C ! Nucleic acid aromatic carbon to amide
+MASS 24   CN3  12.011000 C ! Nucleic acid aromatic carbon 
+MASS 25   CN3A 12.011000 C ! NAD+ aromatic carbon
+MASS 26   CN3B 12.011000 C ! NAD+ aromatic carbon
+MASS 27   CN3C 12.011000 C ! NADH aromatic carbon
+MASS 28   CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
+MASS 29   CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
+MASS 30   CN4  12.011000 C ! Nucleic acid purine C8 and ADE C2  
+MASS 31   CN5  12.011000 C ! Nucleic acid purine C4 and C5
+MASS 32   CN5G 12.011000 C ! Nucleic acid guanine C5
+MASS 33   CN7  12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
+MASS 34   CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'
+MASS 35   CN7C 12.011000 C ! C2' in arabinose 
+MASS 36   CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives 
+MASS 37   CN8  12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
+MASS 38   CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
+MASS 39   CN9  12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
+MASS 40   CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha)
+MASS 41   CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha)
+MASS 42   CNA  12.011000 C ! pure aromatic carbon
+MASS 43   CNA2 12.011000 C ! pure aromatic carbon bound to F
+MASS 44   CN6  12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
+MASS 45   CN7E 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
+MASS 50   NN1  14.007000 N ! Nucleic acid amide nitrogen
+MASS 51   NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha)
+MASS 52   NN2  14.007000 N ! Nucleic acid protonated ring nitrogen
+MASS 53   NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE
+MASS 54   NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha)
+MASS 55   NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
+MASS 56   NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
+MASS 57   NN3  14.007000 N ! Nucleic acid unprotonated ring nitrogen 
+MASS 58   NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
+MASS 59   NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3
+MASS 60   NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3
+MASS 61   NN4  14.007000 N ! Nucleic acid purine N7
+MASS 62   NN5  14.007000 N ! Nucleic acid sp2 amine nitrogen
+MASS 63   NN6  14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
+MASS 70   OT   15.999400 O ! TIPS3P WATER OXYGEN
+MASS 71   ON1  15.999400 O ! Nucleic acid carbonyl oxygen
+MASS 72   ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
+MASS 73   ON2  15.999400 O ! Nucleic acid phosphate ester oxygen
+MASS 74   ON3  15.999400 O ! Nucleic acid =O in phosphate 
+MASS 75   ON4  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
+MASS 76   ON5  15.999400 O ! Nucleic acid ribose hydroxyl oxygen
+MASS 77   ON6  15.999400 O ! Nucleic acid deoxyribose ring oxygen
+MASS 78   ON6B 15.999400 O ! Nucleic acid ribose ring oxygen
+MASS 79   ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str)
+MASS 80   FN1  18.998400 F ! Fluorine for sugar derivatives (NF) 
+MASS 81   FNA  18.998400 F ! Aromatic fluorine
+MASS 82   P    30.974000 P ! phosphorus
+MASS 83   P2   30.974000 P ! pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
+MASS 84   P3   30.974000 P ! protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
+MASS 90   SOD  22.989770 NA ! Sodium Ion
+MASS 91   MG   24.305000 MG ! Magnesium Ion
+MASS 92   POT  39.102000 K  ! Potassium Ion! check masses
+MASS 93   CES 132.900000 CS ! Cesium Ion
+MASS 94   CAL  40.080000 CA ! Calcium Ion
+MASS 95   CLA  35.450000 CL ! Chloride Ion
+MASS 96   ZN   65.370000 ZN ! zinc (II) cation
+MASS 99   DUM   0.001    H ! dummy atom
+MASS 102  CPH1 12.011000 C ! For imidazole model compound (NF)
+MASS 103  CPH2 12.011000 C ! For imidazole model compound (NF)
+MASS 104  HR3   1.008000 H ! For imidazole model compound (NF) 
+MASS 105  HR1   1.008000 H ! For imidazole model compound (NF) 
+MASS 106  NR1  14.007000 H ! For nitrogen in imidazol (NF)
+MASS 107  NR2  14.007000 H ! For nitrogen in imidazol (NF)
+
+DECL  +P  
+DECL  +O1P 
+DECL  +O2P 
+DECL  +O5' 
+DECL  -O3' 
+ 
+DEFA FIRS none LAST none
+AUTOGENERATE ANGLES DIHEDRALS
+                                                  
+RESI GUA         -1.00  !               O6
+ATOM P    P       1.50  !               ||   
+ATOM O1P  ON3    -0.78  !               C6    
+ATOM O2P  ON3    -0.78  !              /  \  
+ATOM O5'  ON2    -0.57  !          H1-N1   C5--N7\\
+ATOM C5'  CN8B   -0.08  !             |    ||     C8-H8
+ATOM H5'  HN8     0.09  !             C2   C4--N9/
+ATOM H5'' HN8     0.09  !            / \\ /      \
+GROUP                   !      H21-N2   N3        \
+ATOM C4'  CN7     0.16  !          |               \
+ATOM H4'  HN7     0.09  !         H22               \
+ATOM O4'  ON6B   -0.50  !                            \
+ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
+ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
+GROUP                   !        -P-O5'-C5'---C4'    C1'
+ATOM N9   NN2B   -0.02  !         |      |     \     / \
+ATOM C4   CN5     0.26  !        O2P    H5''   C3'--C2' H1'
+ATOM N2   NN1    -0.68  !                      / \   / \
+ATOM H21  HN1     0.32  !                     O3' H3' O2' H2'' 
+ATOM H22  HN1     0.35  !                     |       |
+ATOM N3   NN3G   -0.74  !                             H2'
+ATOM C2   CN2     0.75  
+ATOM N1   NN2G   -0.34  
+ATOM H1   HN2     0.26  
+ATOM C6   CN1     0.54 
+ATOM O6   ON1    -0.51
+ATOM C5   CN5G    0.00
+ATOM N7   NN4    -0.60
+ATOM C8   CN4     0.25
+ATOM H8   HN3     0.16
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66 
+ATOM H2'  HN5     0.43 
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM O3'  ON2    -0.57 
+BOND P    O1P       P    O2P       P     O5'
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
+BOND C2   N2        C2   N1        N2   H21
+BOND N2   H22       N1   H1        N1   C6        C6   C5
+BOND C5   N7        C2'  C3'       C3'  O3'       O3'  +P
+BOND C2'  O2'       O2'  H2'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C8   H8  
+DOUBLE   C2  N3     C4   C5        N7   C8        C6   O6
+IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
+DONO H21  N2            
+DONO H22  N2   
+DONO H1   N1   
+DONO H2'  O2'
+ACCE O6   C6         
+ACCE N3    
+ACCE N7    
+ACCE O1P  P
+ACCE O2P  P       
+ACCE O2'  
+ACCE O3'
+ACCE O4'
+ACCE O5'
+! Chi and sugar-phosphate backbone in B-DNA like conformation
+BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
+BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
+BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
+BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
+BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
+BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
+BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
+BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
+BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
+BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
+BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251 !puck
+BILD C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
+BILD O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
+BILD C1'  C4   *N9  C8     1.4896  125.59 -179.99  106.0    1.374    
+BILD C4   N9   C8   N7     1.377   106.0     0.0   113.5    1.304    
+BILD C8   N9   C4   C5     1.374   106.0     0.0   105.6    1.377    
+BILD N9   C5   *C4  N3     1.377   105.6   180.0   128.4    1.355    
+BILD C5   C4   N3   C2     1.377   128.4     0.0   111.8    1.327    
+BILD C4   N3   C2   N1     1.355   111.8     0.0   124.0    1.375    
+BILD N1   N3   *C2  N2     1.375   124.0   180.0   119.7    1.341    
+BILD N3   C2   N2   H21    1.327   119.7   180.0   127.0    1.01     
+BILD H21  C2   *N2  H22    1.01    127.0  -180.0   116.5    1.01     
+BILD N3   C2   N1   C6     1.327   124.0     0.0   124.9    1.393    
+BILD C6   C2   *N1  H1     1.393   124.9   180.0   117.4    1.03     
+BILD C5   N1   *C6  O6     1.415   111.7   180.0   120.0    1.239    
+BILD N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
+BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
+BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
+BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
+BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
+BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
+
+ 
+RESI ADE         -1.00  !             H61  H62!
+ATOM P    P       1.50  !               \  /
+ATOM O1P  ON3    -0.78  !                N6
+ATOM O2P  ON3    -0.78  !                |
+ATOM O5'  ON2    -0.57  !                C6
+ATOM C5'  CN8B   -0.08  !              //  \
+ATOM H5'  HN8     0.09  !              N1   C5--N7\\
+ATOM H5'' HN8     0.09  !              |    ||     C8-H8
+GROUP                   !              C2   C4--N9/
+ATOM C4'  CN7     0.16  !             / \\ /     \
+ATOM H4'  HN7     0.09  !           H2   N3       \
+ATOM O4'  ON6B   -0.50  !                          \
+ATOM C1'  CN7B    0.16  !                           \
+ATOM H1'  HN7     0.09  !                            \
+GROUP                   !        O1P    H5' H4'  O4'  \
+ATOM N9   NN2    -0.05  !         |      |    \ /   \  \
+ATOM C5   CN5     0.28  !        -P-O5'-C5'---C4'    C1'
+ATOM N7   NN4    -0.71  !         |      |     \     / \
+ATOM C8   CN4     0.34  !        O2P    H5''   C3'--C2' H1'
+ATOM H8   HN3     0.12  !                     / \   / \
+ATOM N1   NN3A   -0.74  !                  O3' H3' O2' H2''
+ATOM C2   CN4     0.50  !                   |       |
+ATOM H2   HN3     0.13  !                          H2'
+ATOM N3   NN3A   -0.75  
+ATOM C4   CN5     0.43  
+ATOM C6   CN2     0.46  
+ATOM N6   NN1    -0.77  
+ATOM H61  HN1     0.38  
+ATOM H62  HN1     0.38  
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66 
+ATOM H2'  HN5     0.43 
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM O3'  ON2    -0.57 
+BOND P    O1P       P    O2P       P     O5'
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
+BOND C2   N1        C6   N6
+BOND N6   H61       N6   H62       C6   C5        C5   N7
+BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  +P
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C8   H8        C2   H2
+DOUBLE  N1  C6      C2   N3        C4   C5        N7   C8
+IMPR N6   C6   H61  H62        C6   N1   C5   N6        
+DONO H61  N6   
+DONO H62  N6   
+DONO H2'  O2'
+ACCE N3
+ACCE N7
+ACCE N1            
+ACCE O1P  P
+ACCE O2P  P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
+BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
+BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
+BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
+BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
+BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
+BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
+BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
+BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
+BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
+BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251 !puck
+BILD C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
+BILD O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
+BILD C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367  
+BILD C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312  
+BILD C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382  
+BILD C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
+BILD N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
+BILD C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
+BILD N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342  
+BILD C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337  
+BILD N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01   
+BILD H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01   
+BILD C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337  
+BILD N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01   
+BILD H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01   
+BILD N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
+BILD N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
+BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
+BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
+BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
+BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
+BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
+ 
+RESI CYT         -1.00
+ATOM P    P       1.50  !
+ATOM O1P  ON3    -0.78  !                      H42  H41
+ATOM O2P  ON3    -0.78  !                        \  /    
+ATOM O5'  ON2    -0.57  !                         N4
+ATOM C5'  CN8B   -0.08  !                         |
+ATOM H5'  HN8     0.09  !                         C4
+ATOM H5'' HN8     0.09  !                        /  \\
+GROUP                   !                    H5-C5   N3
+ATOM C4'  CN7     0.16  !                       ||   |
+ATOM H4'  HN7     0.09  !                    H6-C6   C2
+ATOM O4'  ON6B   -0.50  !                        \  / \\
+ATOM C1'  CN7B    0.16  !                         N1   O2
+ATOM H1'  HN7     0.09  !                          \
+GROUP                   !                           \
+ATOM N1   NN2    -0.13  !                            \ 
+ATOM C6   CN3     0.05  !        O1P    H5' H4'  O4'  \
+ATOM H6   HN3     0.17  !         |      |    \ /   \  \
+ATOM C5   CN3    -0.13  !        -P-O5'-C5'---C4'    C1'
+ATOM H5   HN3     0.07  !         |      |     \     / \
+ATOM C2   CN1     0.52  !        O2P    H5''   C3'--C2' H1'
+ATOM O2   ON1C   -0.49  !                     / \   / \ 
+ATOM N3   NN3    -0.66  !                  O3' H3' O2' H2'' 
+ATOM C4   CN2     0.65  !                   |       |
+ATOM N4   NN1    -0.75  !                          H2'
+ATOM H41  HN1     0.37  
+ATOM H42  HN1     0.33  
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66
+ATOM H2'  HN5     0.43 
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM O3'  ON2    -0.57 
+BOND P    O1P       P    O2P       P     O5'
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
+BOND C2   N3        C4   N4        N4   H41       N4   H42
+BOND C4   C5        C2'  C3'       C3'  O3'       O3'  +P
+BOND C2'  O2'       O2'  H2'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C5   H5        C6   H6
+DOUBLE   C2   O2    C5   C6        N3   C4
+IMPR C2   N1   N3   O2        C4   N3   C5   N4
+IMPR N4   C4   H41  H42      
+DONO H42  N4   
+DONO H2'  O2'
+DONO H41  N4   
+ACCE O2   C2
+ACCE N3     
+ACCE O1P  P
+ACCE O2P  P       
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
+BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
+BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
+BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
+BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
+BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
+BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
+BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
+BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
+BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
+BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251
+BILD C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
+BILD O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
+BILD C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364   
+BILD C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337   
+BILD C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356   
+BILD N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237   
+BILD N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334   
+BILD C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337   
+BILD N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01    
+BILD H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01    
+BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
+BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
+BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
+BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
+BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
+BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
+BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
+ 
+RESI THY         -1.00  !                  H51    O4
+ATOM P    P       1.50  !                   |     ||
+ATOM O1P  ON3    -0.78  !               H52-C5M   C4    H3
+ATOM O2P  ON3    -0.78  !                   |  \ /  \  /
+ATOM O5'  ON2    -0.57  !                  H53  C5   N3
+ATOM C5'  CN8B   -0.08  !                       ||   |
+ATOM H5'  HN8     0.09  !                    H6-C6   C2
+ATOM H5'' HN8     0.09  !                        \  / \\  
+GROUP                   !                         N1   O2
+ATOM C4'  CN7     0.16  !                          \
+ATOM H4'  HN7     0.09  !                           \
+ATOM O4'  ON6B   -0.50  !                            \ 
+ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
+ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
+GROUP                   !        -P-O5'-C5'---C4'    C1'
+ATOM N1   NN2B   -0.34  !         |      |     \     / \
+ATOM C6   CN3     0.17  !        O2P    H5''   C3'--C2' H1'
+ATOM H6   HN3     0.17  !                     / \   / \
+ATOM C2   CN1T    0.51  !                   O3' H3' O2' H2''
+ATOM O2   ON1    -0.41  !                    |       | 
+ATOM N3   NN2U   -0.46  !                           H2'
+ATOM H3   HN2     0.36  !
+ATOM C4   CN1     0.50  !
+ATOM O4   ON1    -0.45  !
+ATOM C5   CN3T   -0.15
+ATOM C5M  CN9    -0.11
+ATOM H51  HN9     0.07
+ATOM H52  HN9     0.07
+ATOM H53  HN9     0.07
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66 
+ATOM H2'  HN5     0.43 
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM O3'  ON2    -0.57 
+BOND P    O1P       P    O2P       P     O5'
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
+BOND C2   N3        N3   H3        N3   C4       C4   C5
+BOND C5   C5M       C2'  C3'       C3'  O3'       O3'  +P
+BOND C2'  O2'       O2'  H2'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C6   H6        C5M  H51       C5M  H52       C5M  H53
+DOUBLE  C2   O2     C4   O4        C5   C6
+IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
+DONO H3   N3   
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1P  P
+ACCE O2P  P       
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
+BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
+BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
+BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
+BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284
+BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212
+BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001
+BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996
+BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
+BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
+BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251
+BILD C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
+BILD O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
+BILD C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
+BILD C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
+BILD C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
+BILD N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
+BILD N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
+BILD C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
+BILD C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
+BILD C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
+BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
+BILD C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
+BILD C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
+BILD H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212
+BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284
+BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
+BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
+BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5''   0.0       0.    115.0     0.0    0.0
+ 
+RESI URA         -1.00  !                         O4                               
+ATOM P    P       1.50  !                         ||
+ATOM O1P  ON3    -0.78  !                         C4    H3
+ATOM O2P  ON3    -0.78  !                        /  \  /
+ATOM O5'  ON2    -0.57  !                    H5-C5   N3
+ATOM C5'  CN8B   -0.08  !                       ||   |
+ATOM H5'  HN8     0.09  !                    H6-C6   C2
+ATOM H5'' HN8     0.09  !                        \  / \\    
+GROUP                   !                         N1   O2
+ATOM C4'  CN7     0.16  !                          \
+ATOM H4'  HN7     0.09  !                           \
+ATOM O4'  ON6B   -0.50  !                            \ 
+ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
+ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
+GROUP                   !        -P-O5'-C5'---C4'    C1'
+ATOM N1   NN2B   -0.34  !         |      |     \     / \
+ATOM C6   CN3     0.20  !        O2P    H5''   C3'--C2' H1'
+ATOM H6   HN3     0.14  !                     / \   / \
+ATOM C2   CN1T    0.55  !                   O3' H3' O2' H2''
+ATOM O2   ON1    -0.45  !                    |       | 
+ATOM N3   NN2U   -0.46  !                           H2' 
+ATOM H3   HN2     0.36  !
+ATOM C4   CN1     0.53  !
+ATOM O4   ON1    -0.48  !
+ATOM C5   CN3    -0.15  !
+ATOM H5   HN3     0.10  !
+GROUP
+ATOM C2'  CN7B    0.14
+ATOM H2'' HN7     0.09
+ATOM O2'  ON5    -0.66 
+ATOM H2'  HN5     0.43 
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM O3'  ON2    -0.57 
+BOND P    O1P       P    O2P       P     O5'
+BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
+BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
+BOND C2   N3        N3   H3        N3   C4        C4   C5
+BOND C2'  C3'       C3'  O3'       O3'  +P
+BOND C2'  O2'       O2'  H2'
+BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
+BOND C5'  H5''      C5   H5        C6   H6
+DOUBLE  C2   O2     C4   O4        C5   C6
+IMPR C2   N1   N3   O2        C4   N3   C5   O4
+DONO H3   N3   
+DONO H2'  O2'
+ACCE O2   C2
+ACCE O4   C4
+ACCE O1P  P
+ACCE O2P  P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+BILD -O3' P    O5'  C5'    1.6001  101.45  -39.25  119.00   1.4401
+BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
+BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
+BILD  P   O5'  C5'  C4'    1.5996  119.00 -151.39  110.04   1.5160
+BILD O5'  C5'  C4'  C3'    1.4401  108.83 -179.85  116.10   1.5284
+BILD C5'  C4'  C3'  O3'    1.5160  116.10   76.70  115.12   1.4212
+BILD C4'  C3'  O3'  +P     1.5284  111.92  159.13  119.05   1.6001
+BILD C3'  O3'  +P   +O5'   1.4212  119.05  -98.86  101.45   1.5996
+BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
+BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
+BILD C4'  C3'  C2'  C1'    1.5284  100.16   39.58  102.04   1.5251
+BILD C3'  C2'  C1'  N1     1.5284  101.97  144.39  113.71   1.4896
+BILD O4'  C1'  N1   C2     1.5251  113.71  -96.0   117.06   1.3746
+BILD C1'  C2   *N1  C6     1.4896  117.06 -180.0   121.3    1.379    
+BILD C2   N1   C6   C5     1.379   121.3     0.0   122.8    1.338    
+BILD C6   N1   C2   N3     1.380   121.3     0.0   114.8    1.373    
+BILD N1   N3   *C2  O2     1.379   114.8  -180.0   122.0    1.218    
+BILD N1   C2   N3   C4     1.379   114.8     0.0   127.0    1.383    
+BILD C5   N3   *C4  O4     1.440   114.7   180.0   119.8    1.227    
+BILD C2   C4   *N3  H3     1.373   127.0   180.0   116.5    1.03      
+BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
+BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
+BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212   
+BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284   
+BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
+BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
+BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
+BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
+BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
+ 
+! NOTE the option to regenerate all angles and dihedrals allows
+! the explicit inclusion of the THET and DIHE terms to be omitted
+! even if the PRES is used in a PATCH statement.  It is important to
+! inspect the patches prior to use to determine if they should be used
+! in a GENErate or PATCh statement and/or if the AUTOgeneration of 
+! angles and dihedrals is required.
+! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
+! documentation
+
+PRES DEO1         0.000 ! Patch to make DEOXYribose in PYRIMIDINES
+DELETE ATOM O2'         ! necessary due to auto-generate dihedrals
+
+GROUP ! To correct O4' atom type in DNA (NF)
+ATOM C4'  CN7     0.16  !
+ATOM H4'  HN7     0.09  !
+ATOM O4'  ON6    -0.50  !
+ATOM C1'  CN7B    0.16  !
+ATOM H1'  HN7     0.09  !
+GROUP
+ATOM C2'  CN8    -0.18
+ATOM H2'  HN8     0.09
+ATOM H2'' HN8     0.09
+
+BOND C2'  H2'
+THET C1'  C2'  H2'   C3'  C2'  H2'   H2'  C2'  H2''
+DIHE H2'  C2'  C1'  O4'   H2'  C2'  C1'  N1    H2'  C2'  C1'  H1'
+DIHE H2'  C2'  C3'  C4'   H2'  C2'  C3'  O3'   H2'  C2'  C3'  H3'
+BILD C1'  C3'  *C2' H2' 0.0 0.0 -115.0 0.0 0.0
+
+PRES DEO2         0.000 ! Patch to make DEOXYribose in PURINES
+DELETE ATOM O2'         ! necessary due to auto-generate dihedrals
+
+GROUP ! To correct O4' atom type in DNA (NF) 
+ATOM C4'  CN7     0.16  !
+ATOM H4'  HN7     0.09  !
+ATOM O4'  ON6    -0.50  !
+ATOM C1'  CN7B    0.16  !
+ATOM H1'  HN7     0.09  ! 
+GROUP
+ATOM C2'  CN8    -0.18
+ATOM H2'  HN8     0.09
+ATOM H2'' HN8     0.09
+
+BOND C2'  H2'
+THET C1'  C2'  H2'   C3'  C2'  H2'   H2'  C2'  H2''
+DIHE H2'  C2'  C1'  O4'   H2'  C2'  C1'  N9    H2'  C2'  C1'  H1'
+DIHE H2'  C2'  C3'  C4'   H2'  C2'  C3'  O3'   H2'  C2'  C3'  H3'
+BILD C1'  C3'  *C2' H2' 0.0 0.0 -115.0 0.0 0.0
+
+PRES 5TER         0.00  ! 5'-terminal HYDROXYL patch, from MeOH
+                        ! use in generate statement
+GROUP
+ATOM H5T  HN5     0.43
+ATOM O5'  ON5    -0.66
+ATOM C5'  CN8B    0.05
+ATOM H5'  HN8     0.09 
+ATOM H5'' HN8     0.09 
+!
+DELETE ATOM P
+DELETE ATOM O1P
+DELETE ATOM O2P
+!
+BOND H5T   O5'        
+DONO H5T   O5'
+BILD H5T  O5'   C5'  C4'   0.0000    0.00  180.00    0.00   0.0000
+ 
+PRES 5MET         0.00  ! 5'-ribose METHYL patch
+                        ! use in generate statement
+GROUP
+ATOM C5'  CN9    -0.27
+ATOM H5'  HN9     0.09 
+ATOM H5'' HN9     0.09 
+ATOM H53' HN9     0.09  ! Can't use ''' and avoid conflict with THY
+!              
+DELETE ATOM O5'
+DELETE ATOM P
+DELETE ATOM O1P
+DELETE ATOM O2P
+!
+BOND C5' H53'
+IC  C3'   C4'   C5'   H53'   0.0000    0.00  180.00    0.00   0.0000
+IC  H53'  C4'   *C5'  H5'    0.0000    0.00  120.00    0.00   0.0000
+IC  H53'  C4'   *C5'  H5''   0.0000    0.00 -120.00    0.00   0.0000
+
+PRES 5PHO        -1.00  ! 5'terminal PHOSPHATE patch
+                        ! use in generate statement
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09 
+ATOM H5'' HN8     0.09 
+ATOM P    P       1.50
+ATOM O1P  ON3    -0.82
+ATOM O2P  ON3    -0.82
+ATOM O5'  ON2    -0.62
+ATOM O5T  ON4    -0.68
+ATOM H5T  HN4     0.34
+BOND O5T  P     H5T  O5T      
+DONO H5T  O5T
+! Built in B-DNA-like conformation (NF)
+BILD C4'   C5'  O5' P      0.0000  000.00 -146.00   000.00   0.0000
+BILD C5'   O5'  P   O5T    0.0000  000.00  -46.90   000.00   0.0000
+BILD O5T   O5'  *P  O1P    0.0000  000.00 -115.82   000.00   0.0000
+BILD O5T   O5'  *P  O2P    0.0000  000.00  115.90   000.00   0.0000
+BILD H5T   O5T  P   O5'    0.0000  000.00  -95.20   000.00   0.0000
+                           
+PRES 5POM        -1.00  ! 5'terminal Methyl-Phosphate patch
+                        ! use in generate statement
+GROUP
+ATOM C5'  CN8B   -0.08
+ATOM H5'  HN8     0.09
+ATOM H5'' HN8     0.09
+ATOM P    P       1.50
+ATOM O1P  ON3    -0.78
+ATOM O2P  ON3    -0.78
+ATOM O5'  ON2    -0.57
+ATOM O5T  ON2    -0.57
+ATOM C5T  CN9    -0.17
+ATOM H5T1 HN9     0.09
+ATOM H5T2 HN9     0.09
+ATOM H5T3 HN9     0.09
+
+BOND O5T  P     O5T	C5T	C5T 	H5T1	C5T     H5T2	
+BOND C5T     H5T3
+!DONO H5T  O5T
+! Built in B-DNA-like conformation (NF)
+BILD C4'   C5'  O5' P      0.0000  000.00 -146.00   000.00   0.0000
+BILD C5'   O5'  P   O5T    0.0000  000.00  -46.90   000.00   0.0000
+BILD O5T   O5'  *P  O1P    0.0000  000.00 -115.82   000.00   0.0000
+BILD O5T   O5'  *P  O2P    0.0000  000.00  115.90   000.00   0.0000
+BILD C5T   O5T  P   O5'    0.0000  000.00  -95.20   000.00   0.0000
+BILD H5T1  C5T   O5T  P    0.0000  000.00  180.20   000.00   0.0000
+BILD H5T2  C5T   O5T  P    0.0000  000.00   60.00   000.00   0.0000
+BILD H5T3  C5T   O5T  P    0.0000  000.00  -60.00   000.00   0.0000
+
+PRES 3TER         0.00  ! 3'terminal HYDROXYL patch, from MeOH
+                        ! use in generate statement
+GROUP
+ATOM C3'  CN7     0.14 
+ATOM H3'  HN7     0.09 
+ATOM O3'  ON5    -0.66
+ATOM H3T  HN5     0.43
+BOND O3'  H3T
+DONO H3T  O3'
+BILD H3T  O3'   C3'  C4'   0.9600  114.97  148.63  111.92   1.5284
+             
+PRES 3PHO        -1.00  ! 3'terminal PHOSPHATE patch
+                        ! use in generate statement
+GROUP                   
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09 
+ATOM P3   P       1.50
+ATOM O1P3 ON3    -0.82
+ATOM O2P3 ON3    -0.82
+ATOM O3'  ON2    -0.62
+ATOM O3T  ON4    -0.68
+ATOM H3T  HN4     0.34
+BOND O3'  P3     P3  O1P3   P3  O2P3   P3  O3T  O3T  H3T  
+DONO H3T  O3T                                            
+ACCE O3T
+ACCE O1P2
+ACCE O2P3
+! Build in B-DNA-like conformation (NF)
+BILD C4'   C3'  O3' P3     0.0000  000.00  155.00   000.00   0.0000
+BILD C3'   O3'  P3  O3T    0.0000  000.00  -95.20   000.00   0.0000
+BILD O3T   O3' *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
+BILD O3T   O3' *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
+BILD H3T   O3T  P3  O3'    0.0000  000.00  -46.90   000.00   0.0000
+
+PRES 3POM        -1.00  ! 3'terminal Methyl Phosphate patch
+                        ! use in generate statement
+! To build model compound with OPO3-CH3 at the 3' end (nicolas)
+GROUP
+ATOM C3'  CN7     0.01
+ATOM H3'  HN7     0.09
+ATOM P3   P       1.50
+ATOM O1P3 ON3    -0.78
+ATOM O2P3 ON3    -0.78
+ATOM O3'  ON2    -0.57
+ATOM O3T  ON2    -0.57
+ATOM C3T  CN9    -0.17
+ATOM H3T1 HN9     0.09
+ATOM H3T2 HN9     0.09
+ATOM H3T3 HN9     0.09
+
+BOND O3'  P3     P3   O1P3  P3   O2P3   P3  O3T  O3T C3T 
+BOND C3T  H3T1   C3T  H3T2  C3T  H3T3
+ACCE O3'
+ACCE O5'
+ACCE O1P2
+ACCE O1P3
+BILD C4'   C3'  O3' P3     0.0000  000.00  155.00   000.00   0.0000
+BILD C3'   O3'  P3  O3T    0.0000  000.00  -95.22   000.00   0.0000
+BILD O3T   O3' *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
+BILD O3T   O3' *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
+BILD C3T   O3T  P3  O3'    0.0000  000.00  -46.90   000.00   0.0000
+BILD H3T1  C3T  O3T P3     0.0000  000.00  180.00   000.00   0.0000
+BILD H3T2  C3T  O3T P3     0.0000  000.00   60.00   000.00   0.0000
+BILD H3T3  C3T  O3T P3     0.0000  000.00  -60.00   000.00   0.0000
+
+PRES 3PO3        -2.00  ! 3'terminal PHOSPHATE patch
+                        ! use in generate statement
+			! Added by Nicolas, to be consistent with model componds
+GROUP
+ATOM C3'  CN7    -0.09
+ATOM H3'  HN7     0.09
+ATOM P3   P       1.10
+ATOM O3'  ON2    -0.40
+ATOM O1P3 ON3    -0.90
+ATOM O2P3 ON3    -0.90
+ATOM O3P3 ON3    -0.90
+BOND O3'  P3     P3  O1P3   P3  O2P3   P3  O3P3
+ACCE O1P2
+ACCE O1P3
+BILD C4'  C3'  O3'  P3     0.0000  000.00  180.00   000.00   0.0000
+BILD C3'  O3'  P3   O3P3   0.0000  000.00  -39.52   000.00   0.0000
+BILD O3P3 O3'  *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
+BILD O3P3 O3'  *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
+BILD O3'  P3   O3P3 O3T    0.0000  000.00  180.00   000.00   0.0000
+BILD P3   O3P3 O3T  H3T    0.0000  000.00  180.00   000.00   0.0000
+
+PRES DELB         0.00     ! patch to delete all possible base atoms
+                           ! of Cyt,Gua,Ade,Thy and Ura
+                           !
+!note: error messages will be obtained due to atoms not present in
+!residue being "deleted" by this patch
+!cyt section
+DELE ATOM N1   
+DELE ATOM C6   
+DELE ATOM H6   
+DELE ATOM C2   
+DELE ATOM O2   
+DELE ATOM N3   
+DELE ATOM C4   
+DELE ATOM N4   
+DELE ATOM H41  
+DELE ATOM H42  
+DELE ATOM C5   
+DELE ATOM H5   
+!gua section
+DELE ATOM N9   
+DELE ATOM H1   
+DELE ATOM N2   
+DELE ATOM H21  
+DELE ATOM H22  
+DELE ATOM O6   
+DELE ATOM N7   
+DELE ATOM C8   
+DELE ATOM H8   
+!ade section
+DELE ATOM H2   
+DELE ATOM N6   
+DELE ATOM H61  
+DELE ATOM H62  
+!thy/ura section
+DELE ATOM H3   
+DELE ATOM O4   
+DELE ATOM C5M  
+DELE ATOM H51  
+DELE ATOM H52  
+DELE ATOM H53  
+
+PRES CY35    0.0   ! patch to make a cyclic 3'-5' nucleotide
+                   ! use AUTOGEN ANGLE DIHE after this patch
+BOND O3' P         ! but before water-generation
+
+PRES LKNA    0.0   ! Patch to join to nucleic acid segments (eg for IMAGES)
+                   ! eg: patch sega 10 segb 1
+                   ! sega should have std 3' (gene sega ... last none)
+                   ! segb should have std 5' (gene segb ... first none)
+                   ! USE AUTOgen ANGL DIHE after this patch,
+                   ! but before water-generation
+BOND 1O3'  2P
+!following commented due to use of autogenerate
+!THET 1C3'  1O3'  2P
+!THET 1O3'  2P    2O5'
+!THET 1O3'  2P    2O1P
+!THET 1O3'  2P    2O2P
+!DIHE 1O3'  2P    2O5'  2C5'       1O3'  2P    2O5'  2C5'
+!DIHE 1C4'  1C3'  1O3'  2P
+!DIHE 1C3'  1O3'  2P    2O5'       1C3'  1O3'  2P    2O5'
+IC  1O3'  2P    2O5' 2C5'   1.6001  101.45  -39.25  119.00   1.4401
+IC  1O3'  2O5' *2P   2O1P   1.6001  101.45 -115.82  109.74   1.4802
+IC  1O3'  2O5' *2P   2O2P   1.6001  101.45  115.90  109.80   1.4801
+IC  1C4'  1C3'  1O3' 2P     1.5284  111.92  159.13  119.05   1.6001
+IC  1C3'  1O3'  2P   2O5'   1.4212  119.05  -98.86  101.45   1.5996
+
+RESI TIP3         0.00   ! TIPS3P WATER MODEL  
+                         ! GENERATE USING NOANGLE NODIHEDRAL
+GROUP   
+ATOM OH2  OT     -0.834
+ATOM H1   HT      0.417 
+ATOM H2   HT      0.417  
+BOND OH2  H1     OH2  H2    H1   H2    ! THE LAST BOND IS NEEDED FOR SHAKE
+ANGLE H1 OH2 H2    ! REQUIRED
+ACCEPTOR OH2   
+PATCHING FIRS NONE LAST NONE   
+
+RESI TP3M         0.000  ! "mmff" water model, as an analog of tip3p
+GROUP
+ATOM OH2  OT     -0.834  ! these charges are replaced by the mmff setup
+ATOM H1   HT      0.417  ! these charges are replaced by the mmff setup
+ATOM H2   HT      0.417  ! these charges are replaced by the mmff setup
+BOND OH2 H1 OH2 H2       ! omits the H1-H2 bond, which is needed for shake with tip3p
+ANGLE H1 OH2 H2          ! required
+ACCEPTOR OH2
+PATCHING FIRS NONE LAST NONE
+
+! Ion parameters from Benoit Roux and Coworkers
+! As of 8/98 no NBFIX terms required
+! 
+RESI SOD       1.00 ! Sodium Ion
+GROUP   
+ATOM SOD  SOD  1.00
+PATCHING FIRST NONE LAST NONE   
+
+RESI MG        2.00 ! Magnesium Ion
+GROUP   
+ATOM MG   MG   2.00
+PATCHING FIRST NONE LAST NONE   
+
+RESI POT       1.00 ! Potassium Ion
+GROUP
+ATOM POT   POT 1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CES       1.00 ! Cesium Ion
+GROUP
+ATOM CES  CES  1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CAL       2.00 ! Calcium Ion
+GROUP
+ATOM CAL  CAL  2.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CLA      -1.00 ! Chloride Ion
+GROUP
+ATOM CLA  CLA -1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI ZN2       2.00 ! Zinc ion, Roland Stote
+GROUP
+ATOM ZN   ZN   2.00
+PATCHING FIRST NONE LAST NONE
+
+end
+

tools/ch2lmp/main_manual

@@ -0,0 +1,12 @@
+The charmm2lmp sub-directory contains tools for converting files back-and-forth between
+the CHARMM MD code and LAMMPS.
+
+The charmm2lammps.pl perl script converts CHARMM input files into LAMMPS input.
+The lammps2pdb.pl perl script converts LAMMPS dump files into a pdb series file.
+The mkpdb.f fortran 90 code also converts LAMMPS dump files into PDB files, and the 
+mkdcd.f tool converts LAMMPS dump files into CHARMM *.dcd trajectory files that can
+be read-in to CHARMM for analysis. See the README file in the charmm2lmp sub-directory
+for more information.
+
+These tools were written by Pieter J. in 't Veld (pjintve@sandia.gov) and Paul Crozier
+(pscrozi@sandia.gov) at Sandia.

tools/ch2lmp/other/crd2pdb.pl

@@ -0,0 +1,35 @@
+#!/usr/sbin/perl 
+
+die "Usage: crd2pdb crdfile pdbfile\n" if $#ARGV!=1;
+
+$occ=1.00;
+
+open(CRD, $ARGV[0]) || die "couldn't open $ARGV[0]:$!\n";
+open(PDB, ">$ARGV[1]") || die "couldn't open $ARGV[1]:$!\n";
+
+while (<CRD>)
+	{
+	if (/^\*/)   # comment/header
+		{
+		s/\*\s*(.*)/REMARK $1/;
+		chomp;
+		print PDB "$_\n";
+		}
+	elsif (/^\s*(\d+)\s*$/) # number of atoms
+		{
+		$num_atoms=$1;
+		}
+	else    #coordinate line
+		{
+		($atom_num, $res_num, $res_name, $atom_name, $x,$y,$z, $segment,
+		$res_in_segment, $bfactor)=split(' ');
+#		$res_name =~ s/^(...).*/$1/;
+		printf PDB
+#			"ATOM  %5d %4s %4s  %4d   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s\n",
+			"ATOM  %5d %4s %4s %4d    %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s\n",
+			$atom_num, $atom_name, $res_name, $res_in_segment, $x,$y,$z, 
+			$occ, $bfactor, $segment;
+		}
+		
+	}
+print PDB "END\n";

tools/ch2lmp/other/in_mkdcd

@@ -0,0 +1,10 @@
+10     		:n_con_files
+0    		:n_con_files_to_skip
+1000    		:n_frames_per_con_file
+1				:n_frames_per_dump_to_dcd
+1000			:max_dcd_dumps_per_dcd_file
+0      		:n_dcd_files_to_skip
+31666   	:n_atoms_dump
+31666		:n_atoms_recenter
+/scratch2/pscrozi/dotap/con
+/scratch2/pscrozi/dotap/dotap

tools/ch2lmp/other/in_mkpdb

@@ -0,0 +1,9 @@
+20     :nconfig
+1000   :nper
+19     :nconfig_skip
+1      :nframes_between_pdbs
+33     :nprotein_residues -- # of residues from start used to recenter box
+/enfs/tmp/pscrozi/1/input1
+/enfs/tmp/pscrozi/1/con1_
+/enfs/tmp/pscrozi/1/pdb/h1_
+/enfs/tmp/pscrozi/1/h1_template.pdb

tools/ch2lmp/other/mkdcd.f

@@ -0,0 +1,322 @@
+c -------------------------------------------------------------------------
+c Code converts LAMMPS atom dumps to CHARMM .dcd files
+c Paul Crozier, SNL, 2003-2004
+c -------------------------------------------------------------------------
+
+      module global
+
+      integer, parameter :: max_atoms = 100000
+
+      real x(3,max_atoms)
+
+      real*8 xprd,yprd,zprd,box(2,3)
+
+      integer n_con_files
+      integer n_con_files_to_skip
+      integer n_frames_per_con_file
+      integer n_frames_per_dump_to_dcd
+      integer max_dcd_dumps_per_dcd_file
+      integer n_dcd_files_to_skip
+      integer n_frames
+      integer n_frames_to_skip
+      integer ith_frame
+      integer ith_dump_to_dcd
+      integer n_timesteps
+      integer n_atoms
+      integer n_frozen_atoms
+      integer n_atoms_dump
+      integer n_atoms_recenter
+      integer recenter_flag
+
+      character*76 con_file_path
+      character*76 dcd_file_path
+
+      end module
+
+c -------------------------------------------------------------------------
+c -------------------------------------------------------------------------
+
+      program mkdcd
+      use global
+      implicit none
+
+      call read_in_mkdcd
+
+      do ith_frame = n_frames_to_skip+1, n_frames
+         call find_config
+         call read_config
+         if (recenter_flag == 1) call recenter
+         if (mod(ith_frame,n_frames_per_dump_to_dcd) == 0) call mk_dcd 
+      enddo
+
+      write(6,*) 'Done.'
+      stop
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine find_config
+      use global
+      implicit none
+
+      integer l,m,n,i,j,itag
+
+      real*8  buf(8)
+
+      if (mod((ith_frame-1),n_frames_per_con_file) == 0) then
+        n = (ith_frame-1)/n_frames_per_con_file + 1
+        write(6,*) 'On config file # ', n
+        close(21)
+        if (n < 10) then
+          open(21,file=trim(con_file_path)
+     $      //char(48+n),status='old')
+        elseif (n < 100) then
+          m = n/10
+          n = mod(n,10)
+          open(21,file=trim(con_file_path)
+     $      //char(48+m)//char(48+n),status='old')
+        else
+          l = n/100
+          m = (n - 100*l)/10
+          n = mod(n,10)
+          open(21,file=trim(con_file_path)
+     $      //char(48+l)//char(48+m)//char(48+n),status='old')
+        endif
+        rewind 21
+
+c skip the first frame of each config file
+
+        read(21,*) 
+        read(21,*) n_timesteps
+        read(21,*)
+        read(21,*) n_atoms
+        read(21,*)
+        read(21,*) box(1,1),box(2,1)
+        read(21,*) box(1,2),box(2,2)
+        read(21,*) box(1,3),box(2,3)
+        read(21,*)
+
+        xprd = box(2,1) - box(1,1)
+        yprd = box(2,2) - box(1,2)
+        zprd = box(2,3) - box(1,3)
+
+        if (n_atoms > max_atoms) write(6,*) "n_atoms > max_atoms"
+
+        n_frozen_atoms = 1000000000
+        do i = 1, n_atoms
+           read (21,*) (buf(j),j=1,5)
+           itag = nint(buf(1))
+           n_frozen_atoms = min(itag,n_frozen_atoms)
+        enddo
+
+        n_frozen_atoms = n_frozen_atoms - 1
+
+        recenter_flag = 0        
+        if (n_atoms_recenter < n_atoms) recenter_flag = 1
+
+      endif
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mk_dcd
+      use global
+      implicit none
+
+      real*8 xtlabc(6)
+
+      integer i
+
+      if (mod(ith_dump_to_dcd,max_dcd_dumps_per_dcd_file) == 0) 
+     &  call mk_dcd_start
+
+      ith_dump_to_dcd = ith_dump_to_dcd + 1
+
+      write(6,*) 'Frame # ', ith_frame, 
+     &           ', Dump to .dcd #', ith_dump_to_dcd
+
+      xtlabc(1) = xprd
+      xtlabc(2) = 0.0
+
+      xtlabc(3) = yprd
+      xtlabc(4) = 0.0
+      xtlabc(5) = 0.0
+      xtlabc(6) = zprd
+
+      write(26) xtlabc
+      write(26) (x(1,i), i=1,n_atoms_dump)
+      write(26) (x(2,i), i=1,n_atoms_dump)
+      write(26) (x(3,i), i=1,n_atoms_dump)
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mk_dcd_start
+      use global
+      implicit none
+
+      character*4 hdr
+
+      integer icntrl(20), nstr, n_dcd_file, n, m, l
+
+      write(6,*) 'Creating new .dcd file . . . '
+
+      n_dcd_file = ith_dump_to_dcd/max_dcd_dumps_per_dcd_file +
+     &             n_dcd_files_to_skip + 1
+
+      close(26)
+      if (n_dcd_file < 10) then
+        open(26,file=trim(dcd_file_path)
+     $     //char(48+n_dcd_file)//'.dcd',form='unformatted')
+      elseif (n_dcd_file < 100) then
+        m = n_dcd_file/10
+        n = mod(n_dcd_file,10)
+        open(26,file=trim(dcd_file_path)
+     $     //char(48+m)//char(48+n)//'.dcd',form='unformatted')
+      else
+        l = n_dcd_file/100
+        m = (n_dcd_file - 100*l)/10
+        n = mod(n_dcd_file,10)
+        open(26,file=trim(dcd_file_path)//char(48+l)
+     $      //char(48+m)//char(48+n)//'.dcd',form='unformatted')
+      endif    
+
+      hdr = 'CORD'
+      icntrl = 0
+      nstr = 0					! number of strings in header
+      icntrl(1) = max_dcd_dumps_per_dcd_file	! number of frames in traj file
+      icntrl(2) = 1				! number of steps in previous run
+      icntrl(3) = 1				! frequency of saving
+      icntrl(4) = max_dcd_dumps_per_dcd_file	! total number of steps
+      icntrl(8) = n_atoms_dump*3 - 6			! number of degrees of freedom
+      icntrl(10) = 981668463			! coded time step
+      icntrl(11) = 1				! coded crystallographic group (or zero)
+      icntrl(20) = 28				! CHARMM version number
+
+      write(26) hdr, icntrl
+      write(26) nstr
+      write(26) n_atoms_dump
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+c input data from config file
+
+      subroutine read_config
+      use global
+      implicit none
+
+c local variables
+
+      integer i,j,itag,itrue
+
+      real*8  buf(8)
+
+      read(21,*) 
+      read(21,*) n_timesteps
+      read(21,*)
+      read(21,*) n_atoms
+      read(21,*)
+      read(21,*) box(1,1),box(2,1)
+      read(21,*) box(1,2),box(2,2)
+      read(21,*) box(1,3),box(2,3)
+      read(21,*)
+    
+      xprd = box(2,1) - box(1,1)
+      yprd = box(2,2) - box(1,2)
+      zprd = box(2,3) - box(1,3)
+
+      do i = 1, n_atoms
+         read (21,*) (buf(j),j=1,5)
+         itag = nint(buf(1)) - n_frozen_atoms
+         x(1,itag) = buf(3)*xprd + box(1,1)
+         x(2,itag) = buf(4)*yprd + box(1,2)
+         x(3,itag) = buf(5)*zprd + box(1,3)
+c         x(1,i) = buf(3)*xprd + box(1,1)
+c         x(2,i) = buf(4)*yprd + box(1,2)
+c         x(3,i) = buf(5)*zprd + box(1,3)
+      enddo
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+c read data from in_mkdcd file
+
+      subroutine read_in_mkdcd
+      use global
+      implicit none
+
+ 100  format (a)
+
+      open(22,file='in_mkdcd')
+      rewind 22
+
+      read (22,*) n_con_files
+      read (22,*) n_con_files_to_skip
+      read (22,*) n_frames_per_con_file
+      read (22,*) n_frames_per_dump_to_dcd
+      read (22,*) max_dcd_dumps_per_dcd_file
+      read (22,*) n_dcd_files_to_skip
+      read (22,*) n_atoms_dump
+      read (22,*) n_atoms_recenter
+      read (22,100) con_file_path
+      read (22,100) dcd_file_path
+
+      n_frames = n_con_files * n_frames_per_con_file
+      n_frames_to_skip = n_con_files_to_skip * n_frames_per_con_file
+      ith_frame = n_frames_to_skip
+      ith_dump_to_dcd = 0
+
+      close (22)
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+c recenter box on the average position of the first n_atoms_recenter atoms
+
+      subroutine recenter
+      use global
+      implicit none
+
+      integer i
+      real*8 ave_x, ave_y, ave_z
+      
+      ave_x = 0.0
+      ave_y = 0.0
+      ave_z = 0.0
+      
+      do i = 1, n_atoms_recenter
+         ave_x = ave_x + x(1,i)
+         ave_y = ave_y + x(2,i)
+         ave_z = ave_z + x(3,i)
+      enddo
+      
+      ave_x = ave_x/float(n_atoms_recenter)
+      ave_y = ave_y/float(n_atoms_recenter)
+      ave_z = ave_z/float(n_atoms_recenter)
+      
+      do i = 1, n_atoms_dump
+         x(1,i) = x(1,i) - ave_x
+         x(2,i) = x(2,i) - ave_y
+         x(3,i) = x(3,i) - ave_z
+      enddo
+      
+      do i = 1, n_atoms_dump
+      	x(1,i) = x(1,i) - xprd*(nint(x(1,i)/xprd))
+      	x(2,i) = x(2,i) - yprd*(nint(x(2,i)/yprd))
+      	x(3,i) = x(3,i) - zprd*(nint(x(3,i)/zprd))
+      enddo
+      
+      return
+      end
+
+c -------------------------------------------------------------------------

tools/ch2lmp/other/mkdcd_f77.f

@@ -0,0 +1,352 @@
+c -------------------------------------------------------------------------
+c Code converts LAMMPS atom dumps to CHARMM .dcd files
+c Paul Crozier, SNL, 2003
+c -------------------------------------------------------------------------
+c -------------------------------------------------------------------------
+
+      program mkdcd
+      
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+ 
+      call read_in_mkdcd
+
+      do ith_frame = n_frames_to_skip+1, n_frames
+         call find_config
+         call read_config
+         if (i_recenter_flag == 1) call recenter
+         if (mod(ith_frame,n_frames_per_dump_to_dcd) == 0) call mk_dcd 
+      enddo
+
+      write(6,*) 'Done.'
+      stop
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine find_config
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+ 
+      integer l,m,n,i,j,itag
+
+      real*8  buf(8)
+
+      if (mod((ith_frame-1),n_frames_per_con_file) == 0) then
+        n = (ith_frame-1)/n_frames_per_con_file + 1
+        write(6,*) 'On config file # ', n
+        close(21)
+        if (n < 10) then
+          open(21,file="conf"//char(48+n),status='old')
+        elseif (n < 100) then
+          m = n/10
+          n = mod(n,10)
+          open(21,file="conf"
+     $      //char(48+m)//char(48+n),status='old')
+        else
+          l = n/100
+          m = (n - 100*l)/10
+          n = mod(n,10)
+          open(21,file="conf"
+     $      //char(48+l)//char(48+m)//char(48+n),status='old')
+        endif
+        rewind 21
+
+c skip the first frame of each config file
+
+        read(21,*) 
+        read(21,*) n_timesteps
+        read(21,*)
+        read(21,*) n_atoms
+        read(21,*)
+        read(21,*) box(1,1),box(2,1)
+        read(21,*) box(1,2),box(2,2)
+        read(21,*) box(1,3),box(2,3)
+        read(21,*)
+
+        xprd = box(2,1) - box(1,1)
+        yprd = box(2,2) - box(1,2)
+        zprd = box(2,3) - box(1,3)
+
+        if (n_atoms > max_atoms) write(6,*) "n_atoms > max_atoms"
+
+        n_frozen_atoms = 1000000000
+        do i = 1, n_atoms
+           read (21,*) (buf(j),j=1,5)
+           itag = nint(buf(1))
+           n_frozen_atoms = min(itag,n_frozen_atoms)
+        enddo
+
+        n_frozen_atoms = n_frozen_atoms - 1
+
+        i_recenter_flag = 0        
+        if (n_atoms_recenter < n_atoms) i_recenter_flag = 1
+
+      endif
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mk_dcd
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+      
+      real*8 xtlabc(6)
+
+      integer i
+
+      if (mod(ith_dump_to_dcd,max_dcd_dumps_per_dcd_file) == 0) 
+     &  call mk_dcd_start
+
+      ith_dump_to_dcd = ith_dump_to_dcd + 1
+
+      write(6,*) 'Frame # ', ith_frame, 
+     &           ', Dump to .dcd #', ith_dump_to_dcd
+
+      xtlabc(1) = xprd
+      xtlabc(2) = 0.0
+
+      xtlabc(3) = yprd
+      xtlabc(4) = 0.0
+      xtlabc(5) = 0.0
+      xtlabc(6) = zprd
+
+      write(26) xtlabc
+      write(26) (x(1,i), i=1,n_atoms_dump)
+      write(26) (x(2,i), i=1,n_atoms_dump)
+      write(26) (x(3,i), i=1,n_atoms_dump)
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mk_dcd_start
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+      
+      character*4 hdr
+
+      integer icntrl(20), nstr, n_dcd_file, n, m
+
+      write(6,*) 'Creating new .dcd file . . . '
+
+      n_dcd_file = ith_dump_to_dcd/max_dcd_dumps_per_dcd_file +
+     &             n_dcd_files_to_skip + 1
+
+      m = n_dcd_file/10
+      n = mod(n_dcd_file,10)
+
+      close(26)
+      open(26,file="out"
+     $   //char(48+m)//char(48+n)//'.dcd',form='unformatted')
+
+      hdr = 'CORD'
+      do n = 1,20
+            icntrl(n) = 0
+      enddo
+      nstr = 0					! number of strings in header
+      icntrl(1) = max_dcd_dumps_per_dcd_file	! number of frames in traj file
+      icntrl(2) = 1				! number of steps in previous run
+      icntrl(3) = 1				! frequency of saving
+      icntrl(4) = max_dcd_dumps_per_dcd_file	! total number of steps
+      icntrl(8) = n_atoms_dump*3 - 6			! number of degrees of freedom
+      icntrl(10) = 981668463			! coded time step
+      icntrl(11) = 1				! coded crystallographic group (or zero)
+      icntrl(20) = 28				! CHARMM version number
+
+      write(26) hdr, icntrl
+      write(26) nstr
+      write(26) n_atoms_dump
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+c input data from config file
+
+      subroutine read_config
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+      
+c local variables
+
+      integer i,j,itag,itrue
+
+      real*8  buf(8)
+
+      read(21,*) 
+      read(21,*) n_timesteps
+      read(21,*)
+      read(21,*) n_atoms
+      read(21,*)
+      read(21,*) box(1,1),box(2,1)
+      read(21,*) box(1,2),box(2,2)
+      read(21,*) box(1,3),box(2,3)
+      read(21,*)
+    
+      xprd = box(2,1) - box(1,1)
+      yprd = box(2,2) - box(1,2)
+      zprd = box(2,3) - box(1,3)
+
+      do i = 1, n_atoms
+         read (21,*) (buf(j),j=1,5)
+c         itag = nint(buf(1)) - n_frozen_atoms
+c         x(1,itag) = buf(3)*xprd + box(1,1)
+c         x(2,itag) = buf(4)*yprd + box(1,2)
+c         x(3,itag) = buf(5)*zprd + box(1,3)
+         x(1,i) = buf(3)*xprd + box(1,1)
+         x(2,i) = buf(4)*yprd + box(1,2)
+         x(3,i) = buf(5)*zprd + box(1,3)
+      enddo
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+c read data from in_mkdcd file
+
+      subroutine read_in_mkdcd
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+      
+ 100  format (a)
+
+      open(22,file='in_mkdcd')
+      rewind 22
+
+      read (22,*) n_con_files
+      read (22,*) n_con_files_to_skip
+      read (22,*) n_frames_per_con_file
+      read (22,*) n_frames_per_dump_to_dcd
+      read (22,*) max_dcd_dumps_per_dcd_file
+      read (22,*) n_dcd_files_to_skip
+      read (22,*) n_atoms_dump
+      read (22,*) n_atoms_recenter
+      read (22,100) con_file_path
+      read (22,100) dcd_file_path
+
+      n_frames = n_con_files * n_frames_per_con_file
+      n_frames_to_skip = n_con_files_to_skip * n_frames_per_con_file
+      ith_frame = n_frames_to_skip
+      ith_dump_to_dcd = 0
+
+      close (22)
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+c recenter box on the average position of the first n_atoms_recenter atoms
+
+      subroutine recenter
+      parameter 		(max_atoms = 100000)
+      common/int_variables/	n_con_files, n_con_files_to_skip, 
+     1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
+     2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
+     3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps, 
+     4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
+     5 i_recenter_flag
+      common/real_variables/  xprd, yprd, zprd, box(2,3),  
+     1 x(3,max_atoms)
+	  common/char_variables/ con_file_path, dcd_file_path
+      character*76 con_file_path
+      character*76 dcd_file_path
+      
+      integer i
+      real*8 ave_x, ave_y, ave_z
+      
+      ave_x = 0.0
+      ave_y = 0.0
+      ave_z = 0.0
+      
+      do i = 1, n_atoms_recenter
+         ave_x = ave_x + x(1,i)
+         ave_y = ave_y + x(2,i)
+         ave_z = ave_z + x(3,i)
+      enddo
+      
+      ave_x = ave_x/float(n_atoms_recenter)
+      ave_y = ave_y/float(n_atoms_recenter)
+      ave_z = ave_z/float(n_atoms_recenter)
+      
+      do i = 1, n_atoms_dump
+         x(1,i) = x(1,i) - ave_x
+         x(2,i) = x(2,i) - ave_y
+         x(3,i) = x(3,i) - ave_z
+      enddo
+      
+      do i = 1, n_atoms_dump
+      	x(1,i) = x(1,i) - xprd*(nint(x(1,i)/xprd))
+      	x(2,i) = x(2,i) - xprd*(nint(x(2,i)/yprd))
+      	x(3,i) = x(3,i) - xprd*(nint(x(3,i)/zprd))
+      enddo
+      
+      return
+      end
+
+c -------------------------------------------------------------------------

tools/ch2lmp/other/mkpdb.f

@@ -0,0 +1,469 @@
+c -------------------------------------------------------------------------
+c Code converts LAMMPS output to .pdb files
+c Overlays coordinates from LAMMPS output onto template pdb
+c Assumes atom order is the same between the two
+c Converts from atom-based pbc to residue-based pbc
+c Also assumes starting config fed to LAMMPS had residue-based pbc
+c Paul Crozier, SNL, 2002
+c -------------------------------------------------------------------------
+
+      module global
+
+      real*8 xprd,yprd,zprd,box(2,3)
+
+      real*8, allocatable :: x(:,:),q(:),mass(:)
+      real*8, allocatable :: comx(:),comy(:),comz(:),totmass(:)
+
+      integer ntimestep,natoms,nframes,iframe,nper
+      integer nbonds,nangles,ndihedrals,nimpropers,ntypes
+      integer nbondtypes,nangletypes,ndihedtypes,nimprotypes
+      integer nconfig,nconfig_skip,nskip,nframes_between_pdbs
+      integer nmolecules,nprotein_residues
+
+      integer, allocatable :: mytrue(:,:),type(:),molecule(:)
+      integer, allocatable :: nboxx(:),nboxy(:),nboxz(:)
+
+      character*200 data_file_path,config_file_path,pdb_file_path
+      character*200 compare_file_path
+
+      character*76, allocatable :: outbeg(:),outend(:)
+
+      end module
+
+c -------------------------------------------------------------------------
+c -------------------------------------------------------------------------
+
+      program mkpdb
+      use global
+      implicit none
+
+      call read_in_mkpdb
+      call read_data
+      call mkpdb_start
+
+      do iframe = nskip+1, nframes
+         call find_config
+         call read_config
+         write(6,*) 'Frame # ', iframe
+         if (mod(iframe,nframes_between_pdbs) == 0) call mk_pdb 
+      enddo
+
+      write(6,*) 'Done.'
+      stop
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine find_config
+      use global
+      implicit none
+
+      integer l,m,n,i,j,ntotal
+
+      real*8  buf(8)
+
+      if (mod((iframe-1),nper) == 0) then
+        n = (iframe-1)/nper + 1
+        write(6,*) 'On config file # ', n
+        close(21)
+c        l = n/100
+c        m = n/10 - l*10
+c        n = mod(n,10)
+        open(21,file=trim(config_file_path)
+     $      //char(48+n),status='old')
+        rewind 21
+
+c skip the first frame of each config file
+
+        read(21,*) 
+        read(21,*) ntimestep
+        read(21,*)
+        read(21,*) ntotal
+        read(21,*)
+        read(21,*) box(1,1),box(2,1)
+        read(21,*) box(1,2),box(2,2)
+        read(21,*) box(1,3),box(2,3)
+        read(21,*)
+    
+        if (ntotal /= natoms) write(6,*) 'Mismatch # of atoms'
+
+        do i = 1, natoms
+           read (21,*) (buf(j),j=1,5)
+        enddo
+
+      endif
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      logical function match(str1,str2,m)
+      implicit none
+
+      character*(*) str1,str2
+      integer m
+
+      match = .FALSE.
+      m = len(str1) + 1
+      if (len(str1).gt.len(str2)) return
+      if (str1.eq.str2(1:len(str1))) match = .TRUE.
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mk_pdb
+      use global
+      implicit none
+
+      integer i,j,k,l,m,n,o,imolecule,ith_pdb
+      real*8 xx,yy,zz,shiftx,shifty,shiftz,proteinmass
+
+      ith_pdb = iframe/nframes_between_pdbs
+      j = ith_pdb/1E4
+      k = (ith_pdb - j*1E4)/1E3
+      l = (ith_pdb - j*1E4 - k*1E3)/1E2
+      m = (ith_pdb - j*1E4 - k*1E3 - l*1E2)/1E1
+      n = (ith_pdb - j*1E4 - k*1E3 - l*1E2 - m*1E1)
+
+      open(26,file=trim(pdb_file_path)//char(48+j)//char(48+k)//
+     1              char(48+l)//char(48+m)//char(48+n)//'.pdb')
+
+c Have to convert from pbc applied on an atomic basis to pbc applied
+c on a residue basis.
+
+c Step 1: Recenter system based on protein c.o.m.
+ 
+      shiftx = 0.0
+      shifty = 0.0
+      shiftz = 0.0
+      proteinmass = 0.0
+
+      do i = 1, natoms
+         imolecule = molecule(i)
+         if (imolecule <= nprotein_residues) then
+           shiftx = shiftx + (x(1,i) + mytrue(1,i)*xprd)*mass(type(i))
+           shifty = shifty + (x(2,i) + mytrue(2,i)*yprd)*mass(type(i))
+           shiftz = shiftz + (x(3,i) + mytrue(3,i)*zprd)*mass(type(i))
+           proteinmass = proteinmass + mass(type(i))
+         endif
+      enddo
+
+      shiftx = shiftx/proteinmass 
+      shifty = shifty/proteinmass 
+      shiftz = shiftz/proteinmass 
+
+      do i = 1, natoms
+         x(1,i) = x(1,i) - shiftx
+         x(2,i) = x(2,i) - shifty 
+         x(3,i) = x(3,i) - shiftz
+      enddo
+
+c Step 2: Find the c.o.m. of each residue --- "molecule"
+
+      do i = 1, nmolecules
+         comx(i) = 0.0
+         comy(i) = 0.0
+         comz(i) = 0.0
+         totmass(i) = 0.0
+      enddo
+
+      do i = 1, natoms
+         imolecule = molecule(i)
+         comx(imolecule) = comx(imolecule) + 
+     1                     (x(1,i) + mytrue(1,i)*xprd)*mass(type(i))
+         comy(imolecule) = comy(imolecule) + 
+     1                     (x(2,i) + mytrue(2,i)*yprd)*mass(type(i))
+         comz(imolecule) = comz(imolecule) + 
+     1                     (x(3,i) + mytrue(3,i)*zprd)*mass(type(i))
+         totmass(imolecule) = totmass(imolecule) + mass(type(i))
+      enddo
+
+      do i = 1, nmolecules
+         comx(i) = comx(i)/totmass(i)
+         comy(i) = comy(i)/totmass(i)
+         comz(i) = comz(i)/totmass(i)
+      enddo
+
+c Step 3: Decide how many boxes must be moved in each direction
+
+      do i = 1, nmolecules
+         nboxx(i) = nint(comx(i)/xprd)
+         nboxy(i) = nint(comy(i)/yprd)
+         nboxz(i) = nint(comz(i)/zprd)
+      enddo
+
+c Step 4: Apply moves to atoms. Write pdb file.
+
+      do i = 1, natoms
+         imolecule = molecule(i)
+         xx = x(1,i) + (mytrue(1,i) - nboxx(imolecule))*xprd
+         yy = x(2,i) + (mytrue(2,i) - nboxy(imolecule))*yprd
+         zz = x(3,i) + (mytrue(3,i) - nboxz(imolecule))*zprd 
+         write(26,100) outbeg(i),xx,yy,zz,outend(i)
+      enddo   
+  100 format(a30,3f8.3,a22)
+      write(26,200) 'END'
+  200 format(a3)
+
+      close(26)
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+      subroutine mkpdb_start
+      use global
+      implicit none
+
+      integer i
+      character*76 pdbline(natoms),str
+ 
+      open(25,file=trim(compare_file_path),status='old')
+      rewind 25
+      do i = 1, natoms
+        read(25,100) pdbline(i)
+      enddo
+     
+  100 format (a)
+
+      do i = 1, natoms
+        str = pdbline(i)
+        read (str(1:30),100) outbeg(i)
+        read (str(55:76),100) outend(i)
+      enddo
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+c input data from config file
+
+      subroutine read_config
+      use global
+      implicit none
+
+c local variables
+
+      integer i,j,itag,itrue,ntotal
+
+      real*8  buf(8)
+
+      read(21,*) 
+      read(21,*) ntimestep
+      read(21,*)
+      read(21,*) ntotal
+      read(21,*)
+      read(21,*) box(1,1),box(2,1)
+      read(21,*) box(1,2),box(2,2)
+      read(21,*) box(1,3),box(2,3)
+      read(21,*)
+    
+      if (ntotal /= natoms) write(6,*) 'Mismatch # of atoms'
+
+      xprd = box(2,1) - box(1,1)
+      yprd = box(2,2) - box(1,2)
+      zprd = box(2,3) - box(1,3)
+
+      do i = 1, natoms
+         read (21,*) (buf(j),j=1,5)
+         itag = nint(buf(1))
+         type(itag)= nint(buf(2))
+         x(1,itag) = buf(3)*xprd + box(1,1)
+         x(2,itag) = buf(4)*yprd + box(1,2)
+         x(3,itag) = buf(5)*zprd + box(1,3)
+         mytrue(1,itag) = 0 
+         mytrue(2,itag) = 0
+         mytrue(3,itag) = 0
+      enddo
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+c read data from input file
+
+      subroutine read_data
+      use global
+      implicit none
+
+c local variables
+
+      logical match
+      integer i,j,jtmp,m,itag
+      real*8  buf(7)
+      character*80 str
+
+ 900  format (a)
+
+      open(27,file=trim(data_file_path),status='old')
+      rewind 27
+
+      read (27,*)
+      read (27,*)
+      read (27,*) natoms
+      read (27,*) nbonds
+      read (27,*) nangles
+      read (27,*) ndihedrals
+      read (27,*) nimpropers
+      read (27,*)
+      read (27,*) ntypes
+      if (nbonds.gt.0) read (27,*) nbondtypes
+      if (nangles.gt.0) read (27,*) nangletypes
+      if (ndihedrals.gt.0) read (27,*) ndihedtypes
+      if (nimpropers.gt.0) read (27,*) nimprotypes
+      read (27,*)
+      read (27,*)
+      read (27,*)
+      read (27,*)
+
+      allocate(q(natoms))
+      allocate(type(natoms))
+      allocate(molecule(natoms))
+      allocate(mass(natoms))
+      allocate(x(3,natoms))
+      allocate(mytrue(3,natoms))
+      allocate(outbeg(natoms))
+      allocate(outend(natoms))
+
+      do
+
+        read (27,*,end=999,err=999)
+        read (27,900,end=999,err=999) str
+        read (27,*,end=999,err=999)
+
+        if (match('All Done',str,m)) then
+
+          goto 999
+
+        else if (match('Masses',str,m)) then
+
+          write (6,*) 'Masses ...'
+
+          do i = 1,ntypes
+             read (27,*) jtmp,mass(i)
+          enddo
+
+        else if (match('Atoms',str,m)) then
+
+          write (6,*) 'Atoms ...'
+
+          do i = 1,natoms
+             read (27,*) (buf(j),j=1,7)
+             itag = nint(buf(1))
+             molecule(itag) = nint(buf(2))
+             type(itag) = nint(buf(3))
+             q(itag) = buf(4)
+          enddo
+
+        else if (match('Bonds',str,m)) then
+
+          do i = 1,nbonds
+             read (27,*)
+          enddo
+
+        else if (match('Angles',str,m)) then
+
+          do i = 1,nangles
+             read (27,*)
+          enddo
+
+        else if (match('Impropers',str,m)) then
+
+          do i = 1,nimpropers
+             read (27,*)
+          enddo
+
+        else if (match('Pair Coeffs',str,m)) then
+
+          write (6,*) 'Pair Coeffs ...'
+
+          do i = 1,ntypes
+             read (27,*) 
+          enddo
+
+        else if (match('Bond Coeffs',str,m)) then
+
+          do i = 1,nbondtypes
+             read (27,*)
+          enddo
+
+        else if (match('Angle Coeffs',str,m)) then
+
+          do i = 1,nangletypes
+             read (27,*)
+          enddo
+
+        else if (match('Dihedral Coeffs',str,m)) then
+
+          do i = 1,ndihedtypes
+             read (27,*) 
+          enddo
+
+        else if (match('Dihedrals',str,m)) then
+
+          do i = 1,ndihedrals
+             read (27,*)  
+          enddo
+
+          goto 999
+
+        else
+          write (6,*) 'UNKNOWN: ',trim(str)
+          write (6,*) 'Unknown identifier in data file'
+        endif
+
+      enddo
+
+ 999  continue
+
+      close (27)
+
+      nmolecules = molecule(natoms)
+      allocate(nboxx(nmolecules))
+      allocate(nboxy(nmolecules))
+      allocate(nboxz(nmolecules))
+      allocate(comx(nmolecules))
+      allocate(comy(nmolecules))
+      allocate(comz(nmolecules))
+      allocate(totmass(nmolecules))
+
+      return
+      end
+
+c -------------------------------------------------------------------------
+
+c read data from in_mkpdb file
+
+      subroutine read_in_mkpdb
+      use global
+      implicit none
+
+ 100  format (a)
+
+      open(22,file='in_mkpdb')
+      rewind 22
+
+      read (22,*) nconfig
+      read (22,*) nper
+      read (22,*) nconfig_skip
+      read (22,*) nframes_between_pdbs
+      read (22,*) nprotein_residues
+      read (22,100) data_file_path
+      read (22,100) config_file_path
+      read (22,100) pdb_file_path
+      read (22,100) compare_file_path
+
+      nframes = nconfig*nper
+      nskip = nconfig_skip*nper
+      iframe = nskip
+
+      close (22)
+
+      return
+      end
+
+c -------------------------------------------------------------------------

tools/ch2lmp/other/pdb_to_crd.f

@@ -0,0 +1,98 @@
+c Reads PDB file, writes out charmm file
+c Uses a temp file
+c PDB format
+c text IATOM  TYPE  RES  IRES      X  Y  Z    W
+c  A6   I5  2X A4   A4    I5  4X     3F8.3 6X F6.2
+c charmm format
+c ATOMNO RESNO   RES  TYPE  X     Y     Z   SEGID RESID Weighting
+c   I5    I5  1X A4 1X A4 F10.5 F10.5 F10.5 1X A4 1X A4 F10.5
+c
+c
+        character*80 infile,outfile,line
+        character*4 str1,type,res,code,segid,resid,residold,resold
+        character*1 chain
+        logical loxt(1000)
+        write (6,*) 'Give input PDB files, output will be .crd'
+1       read (5,'(a)') infile
+        i=1
+2       i=i+1
+        if (infile(i:i).eq.' ') then
+         outfile=infile(1:i-1)//'.crd'
+        else
+         goto 2
+        endif
+        open (unit=11, file=infile, status='old')
+        open (unit=12, file='temppdb', status='unknown')
+        open (unit=13, file=outfile, status='new')
+        write (13,'(a80)') '* converted from '//infile
+        write (13,'(a)') '*'
+        do 4 i=1,1000
+4       loxt(i)=.false.
+        nss=0
+        ires=0
+        iat=0
+        residold='    '
+        resold='    '
+        do 100 i=1,100000
+        read (11,'(a80)',end=1000) line
+        read (unit=line,fmt=500) str1
+        if (str1.eq.'SSBO') then
+          nss=nss+1
+          goto 100
+        else if (str1.eq.'ATOM') then
+        iat= iat+1
+        read (unit=line,fmt=500) str1,iatom,type,res,chain,resid,
+     &    x,y,z,a,w,code
+500     format (a4,2x,i5,1x,a4,1x,a4,a1,a4,4x,3f8.3,2f6.2,6x,a4)
+          if ((resid.ne.residold).or.(res.ne.resold)) ires=ires+1
+          residold=resid
+          resold= res
+          if (chain.ne.'    ') then
+            segid=chain//code
+          elseif (code.ne.'    ') then
+            segid=code
+          else
+            segid='MAIN'
+          endif
+          if (type.eq.'CD1 ') then
+             if (res.eq.'ILE ') type='CD  '
+          elseif (type.eq.'OCT1') then
+             type='OT1 '
+          elseif (type.eq.'OCT2') then
+             type='OT2 '
+          elseif (type.eq.'OXT ') then
+             type='OT2 '
+             loxt(ires)=.true.
+          endif
+c fluch resid left
+5         if (resid(1:1).eq.' ') then
+            resid=resid(2:4)//' '
+            goto 5
+          endif
+6         if (type(1:1).eq.' ') then
+            type=type(2:4)//' '
+            goto 6
+          endif
+          write (12,600) iat,ires,res,type,x,y,z,segid,resid,w
+600     format (I5,I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,a4,F10.5)
+        else
+          goto 100
+        endif
+100     continue
+1000    write (6,*) 'Disulfide bonds', nss
+        nres=ires
+        write (13,'(i5)') iat
+        close (unit=12)
+        open (unit=12,file='temppdb',status='old')
+        do 200 i=1,100000
+        read (12,'(a80)',end=2000) line
+        read (unit=line,fmt=600) iatom,ires,res,type,x,y,z,segid,resid,w
+        if (loxt(ires).and.(type.eq.'O   ')) type='OT1 '
+        write (13,600) iatom,ires,res,type,x,y,z,segid,resid,w
+200     continue
+2000    close (unit=11)
+        close (unit=12)
+        close (unit=13)
+        goto 1
+        end
+

tools/chain.f

@@ -0,0 +1,321 @@
+c Create LAMMPS data file for collection of
+c   polymer bead-spring chains of various lengths and bead sizes
+c Syntax: chain < def.chain > data.file
+c   def.chain is input file that specifies the chains
+c   data.file is output file that will be input for LAMMPS
+c includes image flags in data file so chains can be unraveled later
+
+      program chain
+
+      integer swaptype
+      integer, allocatable :: nchain(:),nmonomer(:)
+      integer, allocatable :: ntype(:),nbondtype(:)
+      integer, allocatable :: type(:),molecule(:)
+      integer, allocatable :: imagex(:),imagey(:),imagez(:)
+      real*8, allocatable :: x(:),y(:),z(:)
+      real*8, allocatable :: bondlength(:),restrict(:)
+      common xprd,yprd,zprd,xboundlo,xboundhi,
+     $     yboundlo,yboundhi,zboundlo,zboundhi
+      real*8 random
+ 900  format(a)
+ 901  format(2f10.6,a)
+ 902  format(i3,f5.1)
+ 903  format(i6,i4,i4,3f10.4,3i4)
+ 904  format(i6,i3,2i6)
+
+c read chain definitions
+
+      read (5,*)
+      read (5,*)
+      read (5,*) rhostar
+      read (5,*) iseed
+      read (5,*) nsets
+      read (5,*) swaptype
+
+      allocate(nchain(nsets))
+      allocate(nmonomer(nsets))
+      allocate(ntype(nsets))
+      allocate(nbondtype(nsets))
+      allocate(bondlength(nsets))
+      allocate(restrict(nsets))
+
+      do iset = 1,nsets
+        read (5,*)
+        read (5,*) nchain(iset)
+        read (5,*) nmonomer(iset)
+        read (5,*) ntype(iset)
+        read (5,*) nbondtype(iset)
+        read (5,*) bondlength(iset)
+        read (5,*) restrict(iset)
+      enddo
+
+c natoms = total # of monomers
+
+      natoms = 0
+      do iset = 1,nsets
+        natoms = natoms + nchain(iset)*nmonomer(iset)
+      enddo
+
+      allocate(x(natoms))
+      allocate(y(natoms))
+      allocate(z(natoms))
+      allocate(type(natoms))
+      allocate(molecule(natoms))
+      allocate(imagex(natoms))
+      allocate(imagey(natoms))
+      allocate(imagez(natoms))
+
+c setup box size (sigma = 1.0)
+
+      volume = natoms/rhostar
+      xprd = volume**(1.0/3.0)
+      yprd = xprd
+      zprd = xprd
+
+      xboundlo = -xprd/2.0
+      xboundhi = -xboundlo
+      yboundlo = xboundlo
+      yboundhi = xboundhi
+      zboundlo = xboundlo
+      zboundhi = xboundhi
+
+c generate random chains
+c loop over sets and chains in each set
+      
+      n = 0
+      nmolecule = 0
+
+      do iset = 1,nsets
+        do ichain = 1,nchain(iset)
+          nmolecule = nmolecule + 1
+
+c random starting point for the chain in the box
+
+          x1 = 0.0
+          y1 = 0.0
+          z1 = 0.0
+          x2 = xboundlo + random(iseed)*xprd
+          y2 = yboundlo + random(iseed)*yprd
+          z2 = zboundlo + random(iseed)*zprd
+
+c store 1st monomer of chain
+c 1st monomer is always in original box (image = 0)
+
+          call pbc(x2,y2,z2)
+          n = n + 1
+          x(n) = x2
+          y(n) = y2
+          z(n) = z2
+          type(n) = ntype(iset)
+          imagex(n) = 0
+          imagey(n) = 0
+          imagez(n) = 0
+          if (swaptype == 0) then
+            molecule(n) = nmolecule
+          else
+            molecule(n) = 1
+          endif
+
+c generate rest of monomers in this chain
+
+          do imonomer = 2,nmonomer(iset)
+
+            x0 = x1
+            y0 = y1
+            z0 = z1
+            x1 = x2
+            y1 = y2
+            z1 = z2
+
+c random point inside sphere of unit radius
+
+ 10         xinner = 2.0*random(iseed) - 1.0
+            yinner = 2.0*random(iseed) - 1.0
+            zinner = 2.0*random(iseed) - 1.0
+            rsq = xinner*xinner + yinner*yinner + zinner*zinner
+            if (rsq > 1.0) goto 10
+
+c project point to surface of sphere of unit radius
+
+            r = sqrt(rsq)
+            xsurf = xinner/r
+            ysurf = yinner/r
+            zsurf = zinner/r
+
+c create new point by scaling unit offsets by bondlength (sigma = 1.0)
+
+            x2 = x1 + xsurf*bondlength(iset)
+            y2 = y1 + ysurf*bondlength(iset)
+            z2 = z1 + zsurf*bondlength(iset)
+
+c check that new point meets restriction requirement
+c only for 3rd monomer and beyond
+
+            dx = x2 - x0
+            dy = y2 - y0
+            dz = z2 - z0
+            r = sqrt(dx*dx + dy*dy + dz*dz)
+
+            if (imonomer > 2 .and. r <= restrict(iset)) goto 10
+
+c store new point
+c if delta to previous bead is large, then increment/decrement image flag
+
+            call pbc(x2,y2,z2)
+            n = n + 1
+            x(n) = x2
+            y(n) = y2
+            z(n) = z2
+            type(n) = ntype(iset)
+
+            if (abs(x(n)-x(n-1)) < 2.0*bondlength(iset)) then
+              imagex(n) = imagex(n-1)
+            else if (x(n) - x(n-1) < 0.0) then
+              imagex(n) = imagex(n-1) + 1
+            else if (x(n) - x(n-1) > 0.0) then
+              imagex(n) = imagex(n-1) - 1
+            endif
+
+            if (abs(y(n)-y(n-1)) < 2.0*bondlength(iset)) then
+              imagey(n) = imagey(n-1)
+            else if (y(n) - y(n-1) < 0.0) then
+              imagey(n) = imagey(n-1) + 1
+            else if (y(n) - y(n-1) > 0.0) then
+              imagey(n) = imagey(n-1) - 1
+            endif
+
+            if (abs(z(n)-z(n-1)) < 2.0*bondlength(iset)) then
+              imagez(n) = imagez(n-1)
+            else if (z(n) - z(n-1) < 0.0) then
+              imagez(n) = imagez(n-1) + 1
+            else if (z(n) - z(n-1) > 0.0) then
+              imagez(n) = imagez(n-1) - 1
+            endif
+
+            if (swaptype == 0) then
+              molecule(n) = nmolecule
+            else if (swaptype == 1) then
+              molecule(n) = imonomer
+            else if (swaptype == 2) then
+              if (imonomer <= nmonomer(iset)/2) then
+                molecule(n) = imonomer
+              else
+                molecule(n) = nmonomer(iset)+1-imonomer
+              endif
+            endif
+
+          enddo
+
+        enddo
+      enddo
+
+c compute quantities needed for LAMMPS file
+
+      nbonds = 0
+      ntypes = 0
+      nbondtypes = 0
+      do iset = 1,nsets
+        nbonds = nbonds + nchain(iset)*(nmonomer(iset)-1)
+        if (ntype(iset) > ntypes) ntypes = ntype(iset)
+        if (nbondtype(iset) > nbondtypes)
+     $       nbondtypes = nbondtype(iset)
+      enddo
+
+c write out LAMMPS file
+
+      write (6,900) 'LAMMPS FENE chain data file'
+      write (6,*)
+
+      write (6,*) natoms,' atoms'
+      write (6,*) nbonds,' bonds'
+      write (6,*) 0,' angles'
+      write (6,*) 0,' dihedrals'
+      write (6,*) 0,' impropers'
+      write (6,*)
+
+      write (6,*) ntypes,' atom types'
+      write (6,*) nbondtypes,' bond types'
+      write (6,*) 0,' angle types'
+      write (6,*) 0,' dihedral types'
+      write (6,*) 0,' improper types'
+      write (6,*)
+
+      write (6,901) xboundlo,xboundhi,' xlo xhi'
+      write (6,901) yboundlo,yboundhi,' ylo yhi'
+      write (6,901) zboundlo,zboundhi,' zlo zhi'
+
+      write (6,*)
+      write (6,900) 'Masses'
+      write (6,*)
+
+      do i = 1,ntypes
+        write (6,902) i,1.0
+      enddo
+
+      write (6,*)
+      write (6,900) 'Atoms'
+      write (6,*)
+
+      do i = 1,natoms
+        write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
+     $       imagex(i),imagey(i),imagez(i)
+      enddo
+
+      if (nbonds > 0) then
+
+        write (6,*)
+        write (6,900) 'Bonds'
+        write (6,*)
+
+        n = 0
+        m = 0
+        do iset = 1,nsets
+          do ichain = 1,nchain(iset)
+            do imonomer = 1,nmonomer(iset)
+              n = n + 1
+              if (imonomer /= nmonomer(iset)) then
+                m = m + 1
+                write (6,904) m,nbondtype(iset),n,n+1
+              endif
+            enddo
+          enddo
+        enddo
+
+      endif
+
+      end
+
+c ************
+c Subroutines
+c ************
+
+c periodic boundary conditions - map atom back into periodic box
+
+      subroutine pbc(x,y,z)
+      common xprd,yprd,zprd,xboundlo,xboundhi,
+     $     yboundlo,yboundhi,zboundlo,zboundhi
+
+      if (x < xboundlo) x = x + xprd
+      if (x >= xboundhi) x = x - xprd
+      if (y < yboundlo) y = y + yprd
+      if (y >= yboundhi) y = y - yprd
+      if (z < zboundlo) z = z + zprd
+      if (z >= zboundhi) z = z - zprd
+
+      return
+      end
+
+
+c RNG from Numerical Recipes
+      
+      real*8 function random(iseed)
+      real*8 aa,mm,sseed
+      parameter (aa=16807.0D0,mm=2147483647.0D0)
+      
+      sseed = iseed
+      sseed = mod(aa*sseed,mm)
+      random = sseed/mm
+      iseed = sseed
+
+      return
+      end

tools/data2xmovie.c

@@ -0,0 +1,366 @@
+/* data2xmovie tool
+
+   read LAMMPS data file as input
+   write a snapshot in XMOVIE format
+
+   Syntax:  data2xmovie [options] < infile > outfile
+
+     Options:
+
+     -style atom_style
+
+          use the LAMMPS atom style that corresponds to this file
+	    e.g. atomic or bond or angle or full or eam or granular
+          will be used for reading and writing files
+          if not specified, atom_style = full
+
+      -unmap
+
+          unmap all input atom positions using input image flags
+          image flags must be specified in infile
+	  default is to leave atoms mapped to periodic box
+
+     -inbox xlo xhi ylo yhi zlo zhi
+
+          use these values for the output bounding box of the system
+	    useful if are unmapping atoms into a larger domain
+	  if not specified use the box bounds read in from infile
+*/
+
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+struct box {
+  double xlo,xhi,xsize;
+  double ylo,yhi,ysize;
+  double zlo,zhi,zsize;
+};
+
+#define MAXLINE 1000
+
+#define ATOMIC 1
+#define BOND   2
+#define ANGLE  3
+#define FULL   4
+#define EAM    5
+#define GRANULAR 6
+
+main(int argc, char *argv[])
+
+{
+  char line[1000];            /* strings for reading/parsing input file */
+  char linetoken[1000];
+  char *token;             
+                             /* numbers of various quantities as read in */
+
+  int natoms,nbonds,nangles,ndihedrals,nimpropers;
+  int ntypes,nbondtypes,nangletypes,ndihedtypes,nimprotypes;
+
+  int nmolecules;            /* total # of mols specified by mol tags */
+
+  int atomstyle;             /* atomstyle for read/write of Atoms */
+  int unmap;                 /* 0 = no unmapping, 1 = unmap from input box */
+  int outbox;                /* flag for whether out box is explicitly set */
+
+  struct box in,out;             /* input/output bounding box */
+
+  char *gettoken(char *, int);    /* function defs */
+  void skipline(int); 
+
+  /* default input values */
+
+  atomstyle = 0;
+  unmap = 0;
+  outbox = 0;
+  
+  /* read input options from command line
+     should do more error checking for missing args */
+
+  int i = 1;
+  while (i < argc) {
+
+    if (!strcmp(argv[i],"-style")) {
+      if (strcmp(argv[i+1],"atomic") == 0) atomstyle = ATOMIC;
+      else if (strcmp(argv[i+1],"bond") == 0) atomstyle = BOND;
+      else if (strcmp(argv[i+1],"angle") == 0) atomstyle = ANGLE;
+      else if (strcmp(argv[i+1],"full") == 0) atomstyle = FULL;
+      else if (strcmp(argv[i+1],"eam") == 0) atomstyle = EAM;
+      else if (strcmp(argv[i+1],"granular") == 0) atomstyle = GRANULAR;
+      else {
+	fprintf(stderr,"Error with command-line arg style\n");
+	exit(1);
+      }
+      i += 2;
+    } else if (!strcmp(argv[i],"-unmap")) {
+      unmap = 1;
+      i += 1;
+    } else if (!strcmp(argv[i],"-inbox")) {
+      outbox = 1;
+      sscanf(argv[i+1],"%lg",&out.xlo);
+      sscanf(argv[i+2],"%lg",&out.xhi);
+      sscanf(argv[i+3],"%lg",&out.ylo);
+      sscanf(argv[i+4],"%lg",&out.yhi);
+      sscanf(argv[i+5],"%lg",&out.zlo);
+      sscanf(argv[i+6],"%lg",&out.zhi);
+      i += 7;
+    } else {
+      fprintf(stderr,"Syntax error: data2xmovie [options] < infile > outfile\n");
+      exit(1);
+    }
+  }
+  
+  /* error checks */
+
+  if (atomstyle == 0) {
+    fprintf(stderr,"ERROR: must use -style to set atom style\n");
+    exit(1);
+  }
+
+  /* defaults */
+
+  natoms = nbonds = nangles = ndihedrals = nimpropers = 0;
+  ntypes = nbondtypes = nangletypes = ndihedtypes = nimprotypes = 0;
+
+  /* read header */
+
+  fgets(line,MAXLINE,stdin);
+
+  while (1) {
+    fgets(line,MAXLINE,stdin);
+
+    if (strspn(line," \t\n\r") == strlen(line)) continue;
+    else if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
+    else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
+    else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
+    else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
+    else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
+    else if (strstr(line,"atom types")) sscanf(line,"%d",&ntypes);
+    else if (strstr(line,"bond types")) sscanf(line,"%d",&nbondtypes);
+    else if (strstr(line,"angle types")) sscanf(line,"%d",&nangletypes);
+    else if (strstr(line,"dihedral types")) sscanf(line,"%d",&ndihedtypes);
+    else if (strstr(line,"improper types")) sscanf(line,"%d",&nimprotypes);
+    else if (strstr(line,"xlo xhi")) sscanf(line,"%lg %lg",&in.xlo,&in.xhi);
+    else if (strstr(line,"ylo yhi")) sscanf(line,"%lg %lg",&in.ylo,&in.yhi);
+    else if (strstr(line,"zlo zhi")) sscanf(line,"%lg %lg",&in.zlo,&in.zhi);
+    else break;
+  }
+
+  /* compute input box size */
+
+  in.xsize = in.xhi - in.xlo;
+  in.ysize = in.yhi - in.ylo;
+  in.zsize = in.zhi - in.zlo;
+
+  /* write XMOVIE header */
+
+  printf("ITEM: TIMESTEP\n");
+  printf("%d\n",0);
+  printf("ITEM: NUMBER OF ATOMS\n");
+  printf("%d\n",natoms);
+  printf("ITEM: BOX BOUNDS\n");
+  if (outbox) {
+    printf("%g %g\n",out.xlo,out.xhi);
+    printf("%g %g\n",out.ylo,out.yhi);
+    printf("%g %g\n",out.zlo,out.zhi);
+  } else {
+    printf("%g %g\n",in.xlo,in.xhi);
+    printf("%g %g\n",in.ylo,in.yhi);
+    printf("%g %g\n",in.zlo,in.zhi);
+  }
+
+  /* read identifier strings one by one in free-form part of data file */
+
+  token = gettoken(line,1);
+
+  while (token) {
+
+    /* read atoms */
+
+    if (!strcmp(token,"Atoms")) {
+
+      printf("ITEM: ATOMS\n");
+
+      int tag,type,molecule,imagex,imagey,imagez;
+      double x,y,z,radius,density,q;
+
+      for (i = 0; i < natoms; i++) {
+	fgets(line,MAXLINE,stdin);
+	if (unmap) {
+	  if (atomstyle == ATOMIC) 
+	    sscanf(line,"%d %d %lg %lg %lg %d %d %d",
+		   &tag,&type,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	  else if (atomstyle == BOND) 
+	    sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
+		   &tag,&molecule,&type,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	  else if (atomstyle == ANGLE) 
+	    sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
+		   &tag,&molecule,&type,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	  else if (atomstyle == FULL) 
+	    sscanf(line,"%d %d %d %lg %lg %lg %lg %d %d %d",
+		   &tag,&molecule,&type,&q,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	  else if (atomstyle == EAM) 
+	    sscanf(line,"%d %d %lg %lg %lg %d %d %d",
+		   &tag,&type,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	  else if (atomstyle == GRANULAR) 
+	    sscanf(line,"%d %d %lg %lg %lg %lg %lg %d %d %d",
+		   &tag,&type,&radius,&density,&x,&y,&z,
+		   &imagex,&imagey,&imagez);
+	} else {
+	  if (atomstyle == ATOMIC) 
+	    sscanf(line,"%d %d %d %lg %lg %lg",
+		   &tag,&type,&x,&y,&z);
+	  else if (atomstyle == BOND) 
+	    sscanf(line,"%d %d %d %lg %lg %lg",
+		   &tag,&molecule,&type,&x,&y,&z);
+	  else if (atomstyle == ANGLE) 
+	    sscanf(line,"%d %d %d %lg %lg %lg",
+		   &tag,&molecule,&type,&x,&y,&z);
+	  else if (atomstyle == FULL) 
+	    sscanf(line,"%d %d %d %lg %lg %lg %lg",
+		   &tag,&molecule,&type,&q,&x,&y,&z);
+	  else if (atomstyle == EAM) 
+	    sscanf(line,"%d %d %lg %lg %lg",
+		   &tag,&type,&x,&y,&z);
+	  else if (atomstyle == GRANULAR) 
+	    sscanf(line,"%d %d %lg %lg %lg %lg %lg",
+		   &tag,&type,&radius,&density,&x,&y,&z);
+	  imagez = imagey = imagex = 0;
+	}
+
+	/* unmap atom position if requested */
+
+	if (unmap) {
+	  x = x + imagex*in.xsize;
+	  y = y + imagey*in.ysize;
+	  z = z + imagez*in.zsize;
+	}
+
+	printf("%d %d %g %g %g\n",tag,type,x,y,z);
+      }
+    }
+      
+    /* read bonds and replicate */
+
+    else if (!strcmp(token,"Bonds")) {
+
+      printf("ITEM: BONDS\n");
+
+      int n,btype,bond1,bond2;
+
+      for (i = 0; i < nbonds; i++) {
+	fgets(line,MAXLINE,stdin);
+	sscanf(line,"%d %d %d %d",&n,&btype,&bond1,&bond2);
+	printf("%d %d %d\n",btype,bond1,bond2);
+      }
+    }
+    
+	/* non-replicated sections - just skip lines */
+
+    else if (!strcmp(token,"Velocities"))
+      skipline(natoms);
+    else if (!strcmp(token,"Angles"))
+      skipline(nangles);
+    else if (!strcmp(token,"Dihedrals"))
+      skipline(ndihedrals);
+    else if (!strcmp(token,"Impropers"))
+      skipline(nimpropers);
+    else if (!strcmp(token,"Masses"))
+      skipline(ntypes);
+    else if (!strcmp(token,"Dipoles"))
+      skipline(ntypes);
+    else if (!strcmp(token,"Pair Coeffs"))
+      skipline(ntypes);
+    else if (!strcmp(token,"Bond Coeffs"))
+      skipline(nbondtypes);
+    else if (!strcmp(token,"Angle Coeffs"))
+      skipline(nangletypes);
+    else if (!strcmp(token,"Dihedral Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"Improper Coeffs"))
+      skipline(nimprotypes);
+    else if (!strcmp(token,"BondBond Coeffs"))
+      skipline(nangletypes);
+    else if (!strcmp(token,"BondAngle Coeffs"))
+      skipline(nangletypes);
+    else if (!strcmp(token,"MiddleBondTorsion Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"EndBondTorsion Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"AngleTorsion Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"AngleAngleTorsion Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"BondBond13 Coeffs"))
+      skipline(ndihedtypes);
+    else if (!strcmp(token,"AngleAngle Coeffs"))
+      skipline(nimprotypes);
+    else {
+      fprintf(stderr,
+	      "Error in input data file - unknown identifier %s\n",token);
+      exit(1);
+    }
+
+    token = gettoken(line,0);
+  }
+  
+}
+
+/* ------------------------------------------------------------------- */
+
+/* return a LAMMPS keyword from data file
+   if first is 1, non-blank line with token is in line
+   else read until find a non-blank line
+   keyword is all text on line w/out leading & trailing white space
+   read one additional line after non-blank line (assumed blank)
+   return ptr to keyword
+   return NULL if end of file */
+
+char *gettoken(char *line, int first)
+{
+  char buffer[MAXLINE];
+
+  /* read upto non-blank line plus 1 following line
+     eof is set to 1 if any read hits end-of-file */
+
+  int eof = 0;
+
+  if (!first) if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
+  while (eof == 0 && strspn(line," \t\n\r") == strlen(line))
+    if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
+  if (fgets(buffer,MAXLINE,stdin) == NULL) eof = 1;
+
+  /* if eof, return NULL */
+
+  if (eof) return NULL;
+
+  /* bracket non-whitespace portion of line */
+
+  int start = strspn(line," \t\n\r");
+  int stop = strlen(line) - 1;
+  while (line[stop] == ' ' || line[stop] == '\t' 
+	 || line[stop] == '\n' || line[stop] == '\r') stop--;
+  line[stop+1] = '\0';
+
+  /* return ptr to keyword */
+
+  return &line[start];
+}
+
+/* read n lines and ignore */
+
+void skipline(int n)
+{
+  char line[1000];
+
+  while (n) {
+    fgets(line,MAXLINE,stdin);
+    n--;
+  }
+}

tools/def.chain

@@ -0,0 +1,13 @@
+Polymer chain definition
+
+0.8442          rhostar
+592984          random # seed (8 digits or less)
+1               # of sets of chains (blank line + 6 values for each set)
+0               molecule tag rule: 0 = by mol, 1 = from 1 end, 2 = from 2 ends
+
+320             number of chains
+100             monomers/chain
+1               type of monomers (for output into LAMMPS file)
+1               type of bonds (for output into LAMMPS file)
+0.97            distance between monomers (in reduced units)
+1.02            no distance less than this from site i-1 to i+1 (reduced unit)

tools/def.chain.ab

@@ -0,0 +1,20 @@
+Polymer chain definition
+
+0.6261144       rhostar
+48729           random # seed (8 digits or less)
+2               # of sets of chains (blank line + 6 values for each set)
+0               molecule tag rule: 0 = by mol, 1 = from 1 end, 2 = from 2 ends
+
+8              number of chains
+50              monomers/chain
+1               type of monomers (for output into LAMMPS file)
+1               type of bonds (for output into LAMMPS file)
+0.97            distance between monomers (in reduced units of sigma)
+1.02            no distance less than this from site i-1 to i+1 (reduced unit)
+
+8              number of chains
+50              monomers/chain
+2               type of monomers (for output into LAMMPS file)
+2               type of bonds (for output into LAMMPS file)
+1.17            distance between monomers (in reduced units of sigma)
+1.22            no distance less than this from site i-1 to i+1 (reduced unit)

tools/def.micelle2d

@@ -0,0 +1,9 @@
+2-d micelle definition
+
+0.7             rhostar
+53616456        random # seed (8 digits or less)
+30 30           initial solvent square lattice (nx by ny)
+150             # of solvent to turn into surfactants
+0.75            bond-length of surfactants (units of sigma)
+2               # of tails to add to each head (length of surfactant - 1)
+0               flag for 2nd nearest neighbor bonds (0=no, 1=yes)

tools/lmp2arc/README

@@ -0,0 +1,136 @@
+
+   This program converts a contiguous set of LAMMPS dump (position) files 
+   to a MSI .arc file using a .car file as the template. This enables one to
+   visualize a LAMMPS trajectory using Insight II.
+
+   by Michael Peachey & John Carpenter  (SGI/Cray)
+   currently maintained by Kelly L. Anderson (AFRL/ML)
+   
+   Version 0.1:  8/14/97  MJP
+   Version 1.0:  7/27/98  JEC
+   Version 1.1: 10/22/98  JEC
+   Version 1.2: 11/04/98  JEC
+   Version 1.3:  4/10/05  KLA
+
+
+   1. To build the program
+
+     % cd src
+     % make
+     % cp lmp2arc.exe ../bin
+
+     The program is only a few files so should compile
+     quickly. 
+
+   2. Testing the program
+
+     There are three test jobs in the test directory
+     that one can run
+
+     % ../bin/lmp2arc.exe -car water8.car <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc
+
+     % ../bin/lmp2arc.exe -move_mol -car water8.car <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc.unwrap
+
+     % ../bin/lmp2arc.exe -trueflags -move_mol -car water8.car \
+       <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc.trueflags
+
+     The only differences you should see are date differences.
+
+  3. Usage
+    
+     Usage: lmp2arc.exe [options] -car carfile < infile > outfile
+
+      options
+
+	      -trueflags  (optional)
+
+	         trueflags are present in the LAMMPS position file.
+
+	      -move_mol   (optional)
+
+                 Unwraps molecules. All atoms in the position file are in
+                 the simulation cell. This means that molecules which
+                 are sticking out of the cell will have some of its
+                 atoms "wrapped" to the other side of the periodic cell.
+                 This leads to very messy visualizations. Specification
+                 of -move_mol will attempt to "unwrap" or straighten 
+                 molecules and yield a reasonable visualization. However,
+                 molecules which oscillate around half in or out of the
+                 box may appear to jump from one side of the box to
+                 the other. 
+
+                 Two algorithms are used depending upon the presence of
+                 trueflags. The algorithm that uses trueflags is the
+                 most robust, but the other geometric based algorithm 
+                 should be adequate.
+
+	      -car filename
+
+	         the name of the .car file that corresponds to the
+		 position information. This is required.
+
+	      -skip n   (default is 0)
+
+	         Skip every n timesteps in the position file.
+
+	      -npico n  (default is 2000)
+
+	         Number of timesteps in 1 picosecond of simulation.
+
+              -2001   (default is 2005)
+ 
+                 Version of LAMMPS to convert from.
+                 
+
+	      stdin
+
+	         file containing one or more names of LAMMPS position files
+
+	      stdout
+
+	         the name of the new .arc file
+
+   Examples:
+
+    % lmp2arc.exe -2001 -trueflags -move_mol -skip 4 -car water.car <<EOF > water.arc
+      water1.pos
+      water2.pos
+      EOF
+
+>>>> Program output <<<<<
+
+ lmp2arc v1.2 - LAMMPS MD trajectory to MSI .arc file conversion
+
+
+ Car file name is water.car
+
+ Number of Atoms       = 24
+ Number of Molecules   = 8
+
+ Position file names:
+ water1.pos
+ water2.pos
+
+ Processing Timesteps
+
+ 20 40 60 80 100
+
+ 102 frames were written to the ArcFile
+
+
+ Program Exiting Normally
+
+
+ 4. Questions or comments?
+
+    Send them to Kelly L. Anderson (kelly.anderson@cantab.net)
+

tools/lmp2arc/src/Makefile

@@ -0,0 +1,18 @@
+
+OBJS = lmp2arc.o ReadCarFile.o ProcessPosFile01.o ProcessPosFile05.o unwrap_molecules.o WriteArcFrame.o
+
+lmp2arc.exe: $(OBJS)
+	gcc -o lmp2arc.exe $(OBJS)
+
+lmp2arc.o: lmp2arc.c lmp2.h
+ReadCarFile.o: ReadCarFile.c lmp2.h
+ProcessPosFile01.o: ProcessPosFile01.c lmp2.h
+ProcessPosFile05.o: ProcessPosFile05.c lmp2.h
+WriteArcFrame.o: WriteArcFrame.c lmp2.h
+unwrap_molecules.o: unwrap_molecules.c lmp2.h
+
+.c.o:
+	gcc -O2 -c $<
+
+clean: 
+	rm lmp2arc.exe *.o

tools/lmp2arc/src/ProcessPosFile01.c

@@ -0,0 +1,159 @@
+/****************************** ProcessDumpFile.c ***************************
+*
+*   Created 8/98 by John Carpenter
+*   Based on routines ReadLMPDump and CreateArcFile written by
+*   Mike Peachey during summer 1997
+*
+*   This function reads the output from LAMMPS dumpfile
+*   and then writes it back out to an ACCELRYS arcfile using
+*   info from ReadCarfile.
+*
+*/
+
+#include "lmp2.h"
+
+void ProcessPosFile01(int num_posfiles,char *posnames[],struct Sys *sysinfo,FILE *ArcFile)
+{
+  struct Boundary cell;
+  struct NewAtomCoordinates *coord;
+
+  FILE *PosFile;
+  
+  char line[MAX_LINE_LENGTH];
+
+  int i,iax,itag,itype;
+  int nxx,nyy,nzz,matoms;
+  int frame, mskip,timestep;
+  int ifile;
+
+  float xx,yy,zz;
+
+  /* Function prototype declarations */
+
+  extern void unwrap_molecules(struct NewAtomCoordinates *,struct Sys *);
+  extern void WriteArcFrame(FILE *,int,int,struct Sys *);
+
+  /* Begin execution */
+
+  coord = calloc(sysinfo->natoms, sizeof(struct NewAtomCoordinates));
+  if ( coord == NULL )
+  {
+      fprintf(stderr,"Memory Allocation Problem(coord), exiting program");
+      exit(3);
+  }
+
+  /* process data */
+
+  fprintf(stderr,"\n Processing Timesteps\n\n");
+
+  frame = 0;
+  mskip = 0;
+
+  for (ifile=0; ifile < num_posfiles; ifile++) {
+
+  fprintf(stderr,"\n Opening file \n");
+
+    if ( (PosFile = fopen(posnames[ifile],"r")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",posnames[ifile]);
+      exit(2);
+    }
+
+
+  fprintf(stderr,"\n File open \n");
+
+    while (fgets(line,MAX_LINE_LENGTH, PosFile) != NULL) {
+      if (strstr(line,"NUMBER OF ATOMS")) {   
+	fgets(line,MAX_LINE_LENGTH, PosFile);
+	matoms = atoi(line);
+	if (matoms != sysinfo->natoms) {
+	  fprintf(stderr,"Number of atoms in car and dump files do not match/n");
+	  exit(1);
+	}
+      }
+      else if (strstr(line,"BOX BOUNDS")) {
+
+	for (iax=0; iax < 3; iax++) {
+	  fgets(line, MAX_LINE_LENGTH, PosFile);
+	  cell.low[iax] = atof(strtok(line, " "));
+	  cell.hi[iax]  = atof(strtok(NULL, " \0\n"));
+	  cell.size[iax] = cell.hi[iax] - cell.low[iax];
+	  sysinfo->celldim[iax] = cell.size[iax];
+	}
+      }
+      else if (strstr(line,"TIMESTEP")) {
+
+	fscanf(PosFile,"%d",&timestep);
+      }
+      else if (strstr(line,"ATOMS")) {
+       
+	if (trueflag) {
+	  for (i=0; i<matoms; i++) {
+	    fgets(line, MAX_LINE_LENGTH, PosFile);
+	    sscanf(line,"%d %d %f %f %f %d %d %d",&itag,&itype,
+		   &xx,&yy,&zz,&nxx,&nyy,&nzz);
+
+	    coord[itag-1].type = itype;
+	    coord[itag-1].fract[0]   = xx;
+	    coord[itag-1].fract[1]   = yy;
+	    coord[itag-1].fract[2]   = zz;
+	    coord[itag-1].truef[0]   = nxx;
+	    coord[itag-1].truef[1]   = nyy;
+	    coord[itag-1].truef[2]   = nzz;
+	  }
+
+	  if (move_molecules) unwrap_molecules(coord,sysinfo);
+
+	  for (i=0; i<matoms; i++) {
+	    for (iax=0; iax<3; iax++)
+	      coord[i].fract[iax] += coord[i].truef[iax];
+	  }
+	}
+	else {
+	 
+	  for (i=0; i<matoms; i++) {
+	    fgets(line, MAX_LINE_LENGTH, PosFile);
+	    sscanf(line,"%d %d %f %f %f",&itag,&itype,&xx,&yy,&zz);
+
+	    coord[itag-1].type = itype;
+	    coord[itag-1].fract[0]   = xx;
+	    coord[itag-1].fract[1]   = yy;
+	    coord[itag-1].fract[2]   = zz;
+	  }
+
+	  if (move_molecules) unwrap_molecules(coord,sysinfo);
+
+	} /* end if on trueflag */
+
+	for (i=0; i<matoms; i++) {
+	  sysinfo->atoms[i].xyz[0] = cell.size[0]*coord[i].fract[0];
+	  sysinfo->atoms[i].xyz[1] = cell.size[1]*coord[i].fract[1];
+	  sysinfo->atoms[i].xyz[2] = cell.size[2]*coord[i].fract[2];
+	}
+
+	/* Ready to write arc file entry */
+
+	if ((mskip >= nskip) || (frame == 0)) {
+
+	  WriteArcFrame(ArcFile,frame,timestep,sysinfo);
+	  frame++;
+	  mskip = 0;
+
+	  if (frame%20 == 0) fprintf(stderr," %d",frame);
+	  if (frame%400 == 0) fprintf(stderr,"\n");
+
+	}
+	else
+	  mskip++;
+
+      } /* end if on ITEM */
+
+    } /* end while over LINES*/
+    
+    close(PosFile);
+   
+  } /* end for loop over POS FILES */
+  
+  fprintf(stderr,"\n\n %d frames were written to the ArcFile\n",frame);
+}
+
+	           

tools/lmp2arc/src/ProcessPosFile05.c

@@ -0,0 +1,157 @@
+/****************************** ProcessDumpFile.c ***************************
+*
+*   Created 8/98 by John Carpenter
+*   Based on routines ReadLMPDump and CreateArcFile written by
+*   Mike Peachey during summer 1997
+*
+*   This function reads the output from LAMMPS dumpfile
+*   and then writes it back out to an ACCELRYS arcfile using
+*   info from ReadCarfile.
+*
+*/
+
+#include "lmp2.h"
+
+void ProcessPosFile05(int num_posfiles,char *posnames[],struct Sys *sysinfo,FILE *ArcFile)
+{
+  struct Boundary cell;
+  struct NewAtomCoordinates *coord;
+
+  FILE *PosFile;
+  
+  char line[MAX_LINE_LENGTH];
+
+  int i,iax,itag,itype;
+  int nxx,nyy,nzz,matoms;
+  int frame, mskip,timestep;
+  int ifile;
+
+  float xx,yy,zz;
+
+  /* Function prototype declarations */
+
+  extern void unwrap_molecules(struct NewAtomCoordinates *,struct Sys *);
+  extern void WriteArcFrame(FILE *,int,int,struct Sys *);
+
+  /* Begin execution */
+
+  coord = calloc(sysinfo->natoms, sizeof(struct NewAtomCoordinates));
+  if ( coord == NULL )
+  {
+      fprintf(stderr,"Memory Allocation Problem(coord), exiting program");
+      exit(3);
+  }
+
+  /* process data */
+
+  fprintf(stderr,"\n Processing Timesteps for LAMMPS 2005 dump file\n\n");
+
+  frame = 0;
+  mskip = 0;
+
+  for (ifile=0; ifile < num_posfiles; ifile++) {
+
+    if ( (PosFile = fopen(posnames[ifile],"r")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",posnames[ifile]);
+      exit(2);
+    }
+
+    while (fgets(line,MAX_LINE_LENGTH, PosFile) != NULL) {
+      if (strstr(line,"NUMBER OF ATOMS")) {   
+	fgets(line,MAX_LINE_LENGTH, PosFile);
+	matoms = atoi(line);
+	if (matoms != sysinfo->natoms) {
+	  fprintf(stderr,"Number of atoms in car and dump files do not match\n");
+	  exit(1);
+	}
+      }
+      else if (strstr(line,"BOX BOUNDS")) {
+
+/*
+fprintf(stderr,"HERE 1\n");  
+*/
+	for (iax=0; iax < 3; iax++) {
+	  fgets(line, MAX_LINE_LENGTH, PosFile);
+	  cell.low[iax] = atof(strtok(line, " "));
+	  cell.hi[iax]  = atof(strtok(NULL, " \0\n"));
+	  cell.size[iax] = cell.hi[iax] - cell.low[iax];
+	  sysinfo->celldim[iax] = cell.size[iax];
+	}
+      }
+      else if (strstr(line,"TIMESTEP")) {
+
+	fscanf(PosFile,"%d",&timestep);
+      }
+      else if (strstr(line,"ATOMS")) {
+       
+	if (trueflag) {
+	  for (i=0; i<matoms; i++) {
+	    fgets(line, MAX_LINE_LENGTH, PosFile);
+	    sscanf(line,"%d %d %f %f %f %d %d %d",&itag,&itype,
+		   &xx,&yy,&zz,&nxx,&nyy,&nzz);
+
+	    coord[itag-1].type = itype;
+	    coord[itag-1].fract[0]   = xx;
+	    coord[itag-1].fract[1]   = yy;
+	    coord[itag-1].fract[2]   = zz;
+	    coord[itag-1].truef[0]   = nxx;
+	    coord[itag-1].truef[1]   = nyy;
+	    coord[itag-1].truef[2]   = nzz;
+	  }
+
+	  if (move_molecules) unwrap_molecules(coord,sysinfo);
+
+	  for (i=0; i<matoms; i++) {
+	    for (iax=0; iax<3; iax++)
+	      coord[i].fract[iax] += coord[i].truef[iax];
+	  }
+	}
+	else {
+	 
+	  for (i=0; i<matoms; i++) {
+	    fgets(line, MAX_LINE_LENGTH, PosFile);
+	    sscanf(line,"%d %d %f %f %f",&itag,&itype,&xx,&yy,&zz);
+
+	    coord[itag-1].type = itype;
+	    coord[itag-1].fract[0]   = xx;
+	    coord[itag-1].fract[1]   = yy;
+	    coord[itag-1].fract[2]   = zz;
+	  }
+
+	  if (move_molecules) unwrap_molecules(coord,sysinfo);
+
+	} /* end if on trueflag */
+
+	for (i=0; i<matoms; i++) {
+	  sysinfo->atoms[i].xyz[0] = cell.size[0]*coord[i].fract[0];
+	  sysinfo->atoms[i].xyz[1] = cell.size[1]*coord[i].fract[1];
+	  sysinfo->atoms[i].xyz[2] = cell.size[2]*coord[i].fract[2];
+	}
+
+	/* Ready to write arc file entry */
+
+	if ((mskip >= nskip) || (frame == 0)) {
+
+	  WriteArcFrame(ArcFile,frame,timestep,sysinfo);
+	  frame++;
+	  mskip = 0;
+
+	  if (frame%20 == 0) fprintf(stderr," %d",frame);
+	  if (frame%400 == 0) fprintf(stderr,"\n");
+
+	}
+	else
+	  mskip++;
+
+      } /* end if on ITEM */
+
+    } /* end while over LINES*/
+    
+    close(PosFile);
+   
+  } /* end for loop over POS FILES */
+  
+  fprintf(stderr,"\n\n %d frames were written to the ArcFile\n",frame);
+}
+
+	           

tools/lmp2arc/src/ReadCarFile.c

@@ -0,0 +1,119 @@
+/****************************** ReadCarFile.c ******************************
+*
+*  This function opens the .car file and extracts coordinate information
+*  into the atoms Atom structure
+*
+*  THIS FUNCTION HAS BEEN MODIFIED FROM Msi2LMP2 AND USES THE ATOM
+*  STRUCTURE MEMBERS DIFFERENTLY
+*/
+
+#include "lmp2.h"
+
+void ReadCarFile(FILE *CarF,struct Sys *sysinfo)
+{
+   char line[MAX_LINE_LENGTH];  /* Stores lines as they are read in */
+   int  k,m,n;			/* counters */	
+   int skip;			/* lines to skip at beginning of file */
+
+
+/* Determine Number of molecules & atoms */
+
+   rewind(CarF);
+   sysinfo->no_molecules = -1; /* Set to -1 because counter will be 
+			 incremented an extra time at the end of the file */
+
+   fgets(line,MAX_LINE_LENGTH,CarF); /* Read header line */
+
+/* Check for periodicity, set periodic and skip */
+
+   if( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"PBC=ON",6) == 0)
+   {
+      sysinfo->periodic = 1;
+      skip = 5; /* Data starts 5 lines from beginning of file */
+   }
+   else
+   {
+      sysinfo->periodic = 0;
+      skip = 4;
+   }
+
+/* First pass through file -- Count molecules */
+
+   while( fgets(line,MAX_LINE_LENGTH,CarF) != NULL )
+      if( strncmp(line,"end",3) == 0 ) 
+         sysinfo->no_molecules++;
+
+/* Allocate space to keep track of the number of atoms within a molecule */
+
+   sysinfo->molinfo = 
+     (struct Mol *) calloc(sysinfo->no_molecules,sizeof(struct Mol));
+
+   if ( sysinfo->molinfo == NULL )
+   {
+      puts("Could not allocate memory for molinfo");
+      exit(2);
+   }
+
+/* Second pass through file -- Count atoms */
+
+   rewind(CarF);
+   for(n=0; n < skip; n++)               /* Skip beginning lines */
+      fgets(line,MAX_LINE_LENGTH,CarF);
+
+   sysinfo->molinfo[0].start = 0;
+   sysinfo->molinfo[0].end   = 0;
+   for(n=0; n < sysinfo->no_molecules; n++)
+   {
+      if (n != 0) {
+         sysinfo->molinfo[n].start = sysinfo->molinfo[n-1].end;
+	 sysinfo->molinfo[n].end   = sysinfo->molinfo[n-1].end;
+      }
+      while( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"end",3) ) 
+         sysinfo->molinfo[n].end++;
+   }
+   n = sysinfo->no_molecules-1;
+   sysinfo->natoms = sysinfo->molinfo[n].end; 
+
+/* Allocate space for atoms Atom structures */
+
+   sysinfo->atoms = (struct Atom *) calloc(sysinfo->natoms,
+                                    sizeof(struct Atom));
+   if( sysinfo->atoms == NULL )
+   {
+      puts("Could not allocate memory for AtomList");
+      exit(2);
+   }
+
+/* Third pass through file -- Read+Parse Car File */
+
+   rewind(CarF);
+
+   for(n=0; n < skip; n++)
+      fgets(line,MAX_LINE_LENGTH,CarF);
+
+   for(m=0; m < sysinfo->no_molecules; m++)
+   { /* m loops through molecules */
+      for(n=sysinfo->molinfo[m].start; n < sysinfo->molinfo[m].end; n++)
+      { /* n loops through atoms within a molecule */
+
+         sysinfo->atoms[n].molecule = m;
+
+         fscanf(CarF,"%s %lf %lf %lf %s %s %s %s %f",
+                sysinfo->atoms[n].name,
+                &(sysinfo->atoms[n].xyz[0]),
+                &(sysinfo->atoms[n].xyz[1]),
+                &(sysinfo->atoms[n].xyz[2]),
+		sysinfo->atoms[n].res_name,
+                sysinfo->atoms[n].res_num,
+                sysinfo->atoms[n].potential,
+                sysinfo->atoms[n].element,
+                &(sysinfo->atoms[n].q));
+      } /* End n (atoms) loop */
+
+   fgets(line,MAX_LINE_LENGTH,CarF);
+   fgets(line,MAX_LINE_LENGTH,CarF);
+
+   } /* End m (molecule) loop */
+
+} /* End ReadCarFile() */
+

tools/lmp2arc/src/WriteArcFrame.c

@@ -0,0 +1,63 @@
+#include <time.h>
+#include "lmp2.h"
+
+void WriteArcFrame(FILE *ArcFile,int frame,int timestep,
+                     struct Sys *sysinfo)
+{
+  time_t tim;
+  char *datestr;
+  const char MSIformat[] = "!BIOSYM archive 3";
+  const char PBC_ON[] = "PBC=ON";
+  const char PBC_OFF[] = "PBC=OFF";
+
+  const float perp = 90.0;
+  register int i,m;
+  float number_of_psecs;
+
+  /* Function prototypes */
+
+  void dot(int);
+
+  /* Begin execution */
+
+  number_of_psecs = (float) timestep/(float) npico;
+
+  tim = time(NULL);
+  datestr = asctime(localtime(&tim));
+
+  if (frame == 0) 
+  {
+    fprintf(ArcFile,"%s\n",MSIformat);
+    if (sysinfo->periodic)
+      fprintf(ArcFile,"%s\n",PBC_ON);
+    else
+      fprintf(ArcFile,"%s\n",PBC_OFF);
+  }
+
+  fprintf(ArcFile,"Frame %d  Number of Picoseconds = %10.4f\n",frame,
+                 number_of_psecs);
+
+  fprintf(ArcFile,"!DATE %s",datestr);
+
+  if (sysinfo->periodic) 
+   fprintf(ArcFile,"PBC%10.4f%10.4f%10.4f%10.4f%10.4f%10.4f  (P1)\n", 
+			      sysinfo->celldim[0],sysinfo->celldim[1],
+			      sysinfo->celldim[2],perp,perp,perp);
+
+  for (m=0; m<sysinfo->no_molecules; m++) 
+  {
+    for (i=sysinfo->molinfo[m].start; i<sysinfo->molinfo[m].end; i++)
+    {
+      fprintf(ArcFile,"%-5s %14.9f %14.9f %14.9f %-4s %-7s%-7s %-2s% 6.4f\n",
+              sysinfo->atoms[i].name,
+	      sysinfo->atoms[i].xyz[0],sysinfo->atoms[i].xyz[1],
+	      sysinfo->atoms[i].xyz[2],sysinfo->atoms[i].res_name,
+	      sysinfo->atoms[i].res_num,sysinfo->atoms[i].potential,
+	      sysinfo->atoms[i].element,sysinfo->atoms[i].q);
+    }
+    fprintf(ArcFile, "end\n");
+   }
+   fprintf( ArcFile, "end\n");
+
+   fflush(ArcFile);
+}

tools/lmp2arc/src/lmp2.h

@@ -0,0 +1,72 @@
+# include <stdio.h>
+# include <stdlib.h>
+# include <string.h>
+# include <stddef.h>
+# include <math.h>
+
+#define MAX_LINE_LENGTH   200
+#define MAX_POS_FILES     50
+
+#ifdef MAIN
+#define _EX
+#else
+#define _EX extern  
+#endif
+
+struct Sys {
+  int periodic;
+  int ntypes;
+  int natoms;
+  int no_molecules;
+  int nbonds;
+  float celldim[3];
+  float *masses;
+  struct Mol *molinfo;
+  struct Atom *atoms;
+  int *bondindex;
+};
+  
+struct Mol
+{
+  int start;
+  int end;
+};
+
+struct Atom		/* atom information in .car file */
+{
+  int   molecule;	/* molecule id */
+  float q;              /* charge */
+  double xyz[3];         /* position vector */
+  char  potential[5];	/* atom potential type */
+  char  element[2];     /* atom element */
+  char res_name[8];	/* residue name */
+  char res_num[8];      /* residue numer */
+  char  name[10];       /* atom name */
+};
+
+
+struct Boundary
+{
+  double low[3];
+  double hi[3];
+  double size[3];
+};
+
+struct NewAtomCoordinates
+{
+  int type;
+  double fract[3];
+  int truef[3];
+};
+
+struct Colors
+{
+  float rgb[3];
+};
+
+_EX    int    trueflag;           /* 0=no_true_flags; 1=true_flags */
+_EX    int    move_molecules;     /* 0=don't move; 1=move */
+_EX    int    nskip;              /* number of steps to skip in pos file */
+_EX    int    npico;              /* number of steps per picosecond */
+
+

tools/lmp2arc/src/lmp2arc.c

@@ -0,0 +1,265 @@
+/****************************** Lmp2arc.c ******************************
+
+   This program converts a contiguous set of LAMMPS dump (position) files 
+   to a MSI .arc file using a .car file as the template. This enables one to
+   visualize a LAMMPS trajectory using Insight II.
+
+   by Michael Peachey & John Carpenter  (SGI/Cray)
+   currently maintained by Kelly L. Anderson (AFRL/ML)
+   
+   Version 0.1:  8/14/97  MJP
+   Version 1.0:  7/27/98  JEC
+   Version 1.1: 10/22/98  JEC
+   Version 1.2: 11/04/98  JEC
+   Version 1.3:  4/10/05  KLA
+
+
+   1. To build the program
+
+     % cd src
+     % make
+     % cp lmp2arc.exe ../bin
+
+     The program is only a few files so should compile
+     quickly. 
+
+   2. Testing the program
+
+     There are three test jobs in the test directory
+     that one can run
+
+     % ../bin/lmp2arc.exe -car water8.car <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc
+
+     % ../bin/lmp2arc.exe -move_mol -car water8.car <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc.unwrap
+
+     % ../bin/lmp2arc.exe -trueflags -move_mol -car water8.car \
+       <<EOF > water8.arc
+     > water8.pos
+     > EOF
+     % diff water8.arc correct/water8.arc.trueflags
+
+     The only differences you should see are date differences.
+
+  3. Usage
+    
+     Usage: lmp2arc.exe [options] -car carfile < infile > outfile
+
+      options
+
+	      -trueflags  (optional)
+
+	         trueflags are present in the LAMMPS position file.
+
+	      -move_mol   (optional)
+
+                 Unwraps molecules. All atoms in the position file are in
+                 the simulation cell. This means that molecules which
+                 are sticking out of the cell will have some of its
+                 atoms "wrapped" to the other side of the periodic cell.
+                 This leads to very messy visualizations. Specification
+                 of -move_mol will attempt to "unwrap" or straighten 
+                 molecules and yield a reasonable visualization. However,
+                 molecules which oscillate around half in or out of the
+                 box may appear to jump from one side of the box to
+                 the other. 
+
+                 Two algorithms are used depending upon the presence of
+                 trueflags. The algorithm that uses trueflags is the
+                 most robust, but the other geometric based algorithm 
+                 should be adequate.
+
+	      -car filename
+
+	         the name of the .car file that corresponds to the
+		 position information. This is required.
+
+	      -skip n   (default is 0)
+
+	         Skip every n timesteps in the position file.
+
+	      -npico n  (default is 2000)
+
+	         Number of timesteps in 1 picosecond of simulation.
+
+              -2001   (default is 2005)
+ 
+                 Version of LAMMPS to convert from.
+                 
+
+	      stdin
+
+	         file containing one or more names of LAMMPS position files
+
+	      stdout
+
+	         the name of the new .arc file
+
+   Examples:
+
+    % lmp2arc.exe -2001 -trueflags -move_mol -skip 4 -car water.car <<EOF > water.arc
+      water1.pos
+      water2.pos
+      EOF
+
+>>>> Program output <<<<<
+
+ lmp2arc v1.2 - LAMMPS MD trajectory to MSI .arc file conversion
+
+
+ Car file name is water.car
+
+ Number of Atoms       = 24
+ Number of Molecules   = 8
+
+ Position file names:
+ water1.pos
+ water2.pos
+
+ Processing Timesteps
+
+ 20 40 60 80 100
+
+ 102 frames were written to the ArcFile
+
+
+ Program Exiting Normally
+
+
+ 4. Questions or comments?
+
+    Send them to Kelly L. Anderson (kelly.anderson@cantab.net)
+
+
+*/
+#define MAIN
+#include "lmp2.h" 
+
+ /* External function prototypes */
+   
+   extern void ReadCarFile(FILE *,struct Sys *);
+   extern void ProcessPosFile01(int,char **,struct Sys *,FILE *);
+   extern void ProcessPosFile05(int,char **,struct Sys *,FILE *);
+
+int main(int argc, char *argv[])
+{
+   int got_car,ierr,i;
+   char *carfilename;
+   struct Sys *sysinfo;
+   int num_posfiles;
+   int outv;
+   char *posnames[MAX_POS_FILES];
+   char line[MAX_LINE_LENGTH];
+
+   FILE *CarFile,*ArcFile;
+
+/* default input values */
+
+  trueflag = 0;
+  move_molecules = 0;
+  nskip = 0;
+  got_car = 0;
+  npico = 2000;
+  outv = 2005;
+  
+/* read input options from command line
+   should do more error checking for missing args */
+
+  for (i = 1; i < argc; i++) {
+
+    if (!strcmp(argv[i],"-car")) {
+      carfilename = (char *) malloc(strlen(argv[i+1]));
+      strcpy(carfilename,argv[i+1]);
+      i++;
+      got_car = 1; 
+      }
+    else if (!strcmp(argv[i],"-trueflags"))
+      trueflag = 1;
+    else if (!strcmp(argv[i],"-move_mol"))
+      move_molecules = 1;
+    else if (!strcmp(argv[i],"-2001")) {
+      outv = 2001;
+      fprintf(stderr,"\n LAMMPS 2001 file used.\n"); 
+     }
+    else if (!strcmp(argv[i],"-skip")) {
+      sscanf(argv[i+1],"%d",&nskip);
+      i++;
+      }
+    else if (!strcmp(argv[i],"-npico")) {
+      sscanf(argv[i+1],"%d",&npico);
+      i++;
+      }
+      else {
+      fprintf(stderr,"\nSyntax error: lmp2arc.exe [-2001] [-trueflags] [-move_mol] [-skip n]\n");
+      fprintf(stderr,"                      [-npico m] -car carfile\n");
+      fprintf(stderr,"                      < posfile_list > ArcFile\n");
+      exit(1);
+      }
+  }
+
+/* Check for option inconsistancies */
+
+  if (!got_car) {
+     fprintf(stderr,"Must specify car file\n");
+     exit(1);
+  }
+
+   fprintf(stderr,"\n lmp2arc v1.3 - LAMMPS MD trajectory to ACCELRYS .arc file conversion\n\n");
+
+   sysinfo = (struct Sys *) calloc(1,sizeof(struct Sys));
+
+   /* Open CarFile */
+
+   fprintf(stderr,"\n Car file name is %s\n",carfilename);
+   if( (CarFile = fopen(carfilename,"r")) == NULL )
+   {
+      fprintf(stderr,"Cannot open %s\n",carfilename);
+      exit(2);
+   }
+
+   ReadCarFile(CarFile, sysinfo);
+
+   fclose(CarFile);
+   free(carfilename);
+
+   fprintf(stderr,"\n Number of Atoms       = %d\n",sysinfo->natoms);
+   fprintf(stderr," Number of Molecules   = %d\n",sysinfo->no_molecules);
+
+   /* Get position file names */
+
+   num_posfiles = 0;
+   while (gets(line) != NULL) {
+     if (ferror(stdin) == 0) {
+       posnames[num_posfiles] = (char *)calloc(strlen(line),sizeof(char));
+       posnames[num_posfiles] = strcpy(posnames[num_posfiles],line);
+       num_posfiles++;
+     }
+     else
+       perror(strerror(ferror(stdin)));
+   }
+
+   fprintf(stderr,"\n Position file names:\n");
+   for (i=0;i < num_posfiles; i++) fprintf(stderr," %s\n",posnames[i]);
+
+   /* Assign ArcFile to stdout */
+
+   ArcFile = stdout;
+
+   if (outv == 2001) {  
+       ProcessPosFile01(num_posfiles,posnames,sysinfo,ArcFile); 
+   }
+   else if (outv == 2005) {  
+       ProcessPosFile05(num_posfiles,posnames,sysinfo,ArcFile); 
+   }
+
+   fclose(ArcFile);
+
+   free(sysinfo);
+
+   fprintf(stderr,"\n\n Program Exiting Normally\n\n");
+}

tools/lmp2arc/src/lmp2arc.doc

@@ -0,0 +1,94 @@
+
+   lmp2arc.exe
+
+   by Michael Peachey & John Carpenter  (SGI/Cray)
+   
+   Version 0.1:  8/14/97  MJP   initial version  NVT only
+   Version 1.0:  7/27/98  JEC   rewrote to reduce storage and generalize programs
+   Version 1.1: 10/22/98  JEC   geometric molecule "unwrapping" algorithm included
+   Version 1.2: 11/04/98  JEC   multiple position files in input; data structures
+                                standardized with lmp2gxf
+
+   This program converts a LAMMPS dump (position) file to a MSI
+   .arc file using a .car file as the template. This enables one to
+   visualize a LAMMPS trajectory using Insight II.
+
+    Usage: lmp2arc.exe [options] -car carfile < infile > outfile
+
+      options
+
+	      -trueflags  (default is not present)
+
+	         trueflags are present in the LAMMPS position file.
+
+	      -move_mol   (default is not present)
+
+                 Unwraps molecules. All atoms in the position file are in
+                 simulation cell. This means that molecules which
+                 are sticking out of the cell will have some of its
+                 atoms "wrapped" to the other side of the periodic cell.
+                 This leads to very messy visualizations. Specification
+                 of -move_mol will attempt to "unwrap" or straighten 
+                 molecules and yield a reasonable visualization. However,
+                 molecules which oscillate around half in or out of the
+                 box may appear to jump from one side of the box to
+                 the other. 
+
+                 Two algorithms are used depending upon the presence of
+                 trueflags. The algorithm that uses trueflags is the
+                 most robust, but the other geometric based algorithm 
+                 should be adequate.
+
+	      -car filename
+
+	         the name of the .car file that corresponds to the
+		 position information. This is required.
+
+	      -skip n   (default is 0)
+
+	         Skip every n timesteps in the position file.
+
+	      -npico n  (default is 2000)
+
+	         Number of timesteps in 1 picosecond of simulation
+                 
+
+	      stdin
+
+	         file containing one or more names of LAMMPS position files
+
+	      stdout
+
+	         the name of the new .arc file
+
+   Examples:
+
+    % lmp2arc.exe -trueflags -move_mol -skip 4 -car water.car <<EOF > water.arc
+      water1.pos
+      water2.pos
+      EOF
+
+>>>> Program output <<<<<
+
+ lmp2arc v1.2 - LAMMPS MD trajectory to MSI .arc file conversion
+
+
+ Car file name is water.car
+
+ Number of Atoms       = 24
+ Number of Molecules   = 8
+
+ Position file names:
+ water1.pos
+ water2.pos
+
+ Processing Timesteps
+
+ 20 40 60 80 100
+
+ 102 frames were written to the ArcFile
+
+
+ Program Exiting Normally
+
+

tools/lmp2arc/src/unwrap_molecules.c

@@ -0,0 +1,105 @@
+#include "lmp2.h"
+
+void unwrap_molecules(struct NewAtomCoordinates *coord,struct Sys *sysinfo)
+{
+  int iflag[5],nflag[5],icase;
+  register int i,iax,imol;
+  int min_true,max_true;
+
+  if (trueflag) {
+
+    /* Use trueflags to "unwrap" molecules */
+
+    for (imol=0; imol < sysinfo->no_molecules; imol++) {
+      for (iax=0; iax < 3; iax++) {
+
+	min_true =  1000;
+	max_true = -1000;
+	for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+	     i++) {
+	  if (coord[i].truef[iax] < min_true) min_true = coord[i].truef[iax];
+	  if (coord[i].truef[iax] > max_true) max_true = coord[i].truef[iax];
+	}
+
+	if ((min_true > 0) || (max_true < 0)) {
+	  for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+	       i++) coord[i].truef[iax] -= min_true;
+	}
+
+      } /* end loop over iax */
+    } /* end loop over imol */
+  }
+  else {
+
+    /* Use coordinates to "unwrap" molecules */
+
+    for (imol=0; imol < sysinfo->no_molecules; imol++) {
+
+      for (iax=0; iax < 3; iax++) {
+
+	for (i=0; i<5; i++) { iflag[i] = 0; nflag[i] = 0;}
+
+	for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+	     i++) {
+	  if (coord[i].fract[iax] <= 0.20) 
+	    nflag[0]++;
+	  else if ((coord[i].fract[iax] > 0.20) && (coord[i].fract[iax] <= 0.40))
+	    nflag[1]++;
+	  else if ((coord[i].fract[iax] > 0.40) && (coord[i].fract[iax] <= 0.60))
+	    nflag[2]++;
+	  else if ((coord[i].fract[iax] > 0.60) && (coord[i].fract[iax] <= 0.80))
+	    nflag[3]++;
+	  else if ((coord[i].fract[iax] > 0.80) && (coord[i].fract[iax] <= 1.00))
+	    nflag[4]++;
+	}
+      
+	for (i=0; i<5; i++) { if (nflag[i] > 0) iflag[i] = 1; }
+
+	icase = 10000*iflag[0] + 1000*iflag[1] + 100*iflag[2] + 10*iflag[3] + iflag[4];
+
+	switch (icase) {
+	 case 10001:
+	   if (nflag[0] > nflag[4]) {
+	     for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		  i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
+	   }
+	   else {
+	     for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		  i++) if (coord[i].fract[iax] <= 0.20) coord[i].fract[iax] += 1.0;
+	   }
+	   break;
+         case 11001:
+	   for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
+	   break;
+         case 10011:
+	   for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		i++) if (coord[i].fract[iax] < 0.20) coord[i].fract[iax] += 1.0;
+	   break;
+         case 11101:
+	   for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
+	   break;
+         case 10111:
+	   for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		i++) if (coord[i].fract[iax] < 0.20) coord[i].fract[iax] += 1.0;
+	   break;
+         case 11011:
+	   if ((nflag[0]+nflag[1]) > (nflag[3]+nflag[4])) {
+	     for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		  i++) if (coord[i].fract[iax] > 0.60) coord[i].fract[iax] -= 1.0;
+	   }
+	   else {
+	     for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end; 
+		  i++) if (coord[i].fract[iax] <= 0.40) coord[i].fract[iax] += 1.0;
+	   }
+	   break;
+         default:
+	   break;
+	} /* end switch */
+
+      } /* end loop over imol*/
+    } /* end loop over iax */
+
+  } /* end if on trueflag */
+}

tools/lmp2arc/test/correct/water8.arc

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    0.543599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    0.960479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024    6.987024021    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    0.282672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873    7.105968189 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    0.762192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    0.297000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090    6.606071806    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910    6.505488110    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    0.095184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    0.432575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    0.834192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106    6.820991850    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    0.205056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958    7.154640198 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    0.762192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    0.226511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860    6.760512114    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165    6.874415874    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    0.183599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    0.512136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    0.869832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015    6.869520092    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    0.212472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016    7.140239954 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    0.747576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    0.055799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006    6.742800093    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168    6.942888165    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    0.181008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    0.434880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    0.704520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000    6.811992073    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    0.278639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170    7.108271885 WTR  8      o*      O -0.8200
+H11      3.265271902    0.012384000    0.677304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    0.240624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    0.609695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    0.977183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040    6.958584023    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    0.045288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    0.680471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    0.608328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    0.776808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080    6.987744141    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    0.433007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834    7.023744106 WTR  8      o*      O -0.8200
+H11      3.261815929    0.039672000    0.588599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    0.059904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    0.654839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    0.975168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990    7.193879843    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    0.124992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123    7.096392059 WTR  8      o*      O -0.8200
+H11      3.188807917    0.012960000    0.819000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    0.139176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    0.735695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    1.294919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006    7.088184071    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    0.056159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984    6.358464003    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    0.539423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819    7.138728046 WTR  8      o*      O -0.8200
+H11      3.124296069    0.137015994    0.811223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    0.202175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    0.719496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    1.229760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070    7.096752119    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943    7.141032171 WTR  8      o*      O -0.8200
+H11      3.352391982    0.191015996    0.712007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    0.328680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    0.118223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074    6.558336210    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    0.547056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189    7.157231855 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    0.804456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    0.115200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Thu Sep  6 15:29:47 2001
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    0.639863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    0.928439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053    7.034184122    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    0.033984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071    6.529679918    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    0.501767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149    7.132535791 WTR  8      o*      O -0.8200
+H11      3.196944022    0.108216003    0.712584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    0.271296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2arc/test/correct/water8.arc.trueflags

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    7.743599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    8.160479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024    6.987024021    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    7.482672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873    7.105968189 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    7.962192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    7.497000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090   -0.593928194    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910   -0.694511890    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    0.095184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    7.632575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    8.034192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106    6.820991850    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    7.405056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958    7.154640198 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    7.962192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    7.426511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860   -0.439487886    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165   -0.325584126    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    0.183599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    7.712136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    8.069832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015    6.869520092    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    7.412472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016    7.140239954 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    7.947576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    7.255799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006   -0.457199907    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168   -0.257111835    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    0.181008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    7.634880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    7.904520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000    6.811992073    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    7.478639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170    7.108271885 WTR  8      o*      O -0.8200
+H11      3.265271902    7.212384000    7.877304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    7.440624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    7.809695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    8.177183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040    6.958584023    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    7.245288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    7.880471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    7.808328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    7.976808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080    6.987744141    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    7.633007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834    7.023744106 WTR  8      o*      O -0.8200
+H11      3.261815929    7.239672000    7.788599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    7.259904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    7.854839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    8.175168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990    7.193879843    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    7.324992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123    7.096392059 WTR  8      o*      O -0.8200
+H11      3.188807917    7.212960000    8.019000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    7.339176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    7.935695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    8.494919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006    7.088184071    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    7.256159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984    6.358464003    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    7.739423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819    7.138728046 WTR  8      o*      O -0.8200
+H11      3.124296069    7.337015994    8.011223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    7.402175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    7.919496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    8.429760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070    7.096752119    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943    7.141032171 WTR  8      o*      O -0.8200
+H11      3.352391982    7.391015996    7.912007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    7.528680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    7.318223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074    6.558336210    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    7.747056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189    7.157231855 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    8.004456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    7.315200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Fri Oct  9 14:19:16 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    7.839863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    8.128439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053    7.034184122    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    7.233984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071    6.529679918    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    7.701767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149    7.132535791 WTR  8      o*      O -0.8200
+H11      3.196944022    7.308216003    7.912584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    7.471296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2arc/test/correct/water8.arc.unwrap

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    0.543599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    0.960479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024   -0.212975979    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    7.482672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873   -0.094031811 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    0.762192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    0.297000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090    6.606071806    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910    6.505488110    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    7.295184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    0.432575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    0.834192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106   -0.379008150    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    7.405056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958   -0.045359802 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    0.762192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    0.226511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860    6.760512114    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165    6.874415874    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    7.383599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    0.512136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    0.869832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015   -0.330479908    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    7.412472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016   -0.059760046 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    0.747576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    0.055799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006    6.742800093    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168    6.942888165    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    7.381008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    0.434880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    0.704520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000   -0.388007927    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    7.478639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170   -0.091728115 WTR  8      o*      O -0.8200
+H11      3.265271902    7.212384000    0.677304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    0.240624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    0.609695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    0.977183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040   -0.241415977    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    7.245288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    7.880471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    0.608328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    0.776808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080   -0.212255859    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    7.633007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834   -0.176255894 WTR  8      o*      O -0.8200
+H11      3.261815929    7.239672000    0.588599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    0.059904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    0.654839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    0.975168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990   -0.006120157    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    7.324992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123   -0.103607941 WTR  8      o*      O -0.8200
+H11      3.188807917    7.212960000    0.819000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    0.139176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    0.735695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    1.294919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006   -0.111815929    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    0.056159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984   -0.841535997    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    0.539423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819   -0.061271954 WTR  8      o*      O -0.8200
+H11      3.124296069    7.337015994    0.811223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    0.202175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    0.719496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    1.229760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070   -0.103247881    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943   -0.058967829 WTR  8      o*      O -0.8200
+H11      3.352391982    7.391015996    0.712007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    0.328680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    0.118223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074   -0.641663790    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    0.547056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189   -0.042768145 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    0.804456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    0.115200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Tue Oct 13 14:43:59 1998
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    0.639863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    0.928439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053   -0.165815878    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    0.033984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071   -0.670320082    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    0.501767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149   -0.067464209 WTR  8      o*      O -0.8200
+H11      3.196944022    7.308216003    0.712584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    0.271296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2arc/test/water8.arc

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    0.543599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    0.960479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024    6.987024021    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    0.282672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873    7.105968189 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    0.762192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    0.297000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090    6.606071806    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910    6.505488110    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    0.095184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    0.432575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    0.834192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106    6.820991850    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    0.205056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958    7.154640198 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    0.762192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    0.226511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860    6.760512114    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165    6.874415874    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    0.183599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    0.512136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    0.869832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015    6.869520092    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    0.212472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016    7.140239954 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    0.747576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    0.055799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006    6.742800093    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168    6.942888165    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    0.181008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    0.434880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    0.704520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000    6.811992073    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    0.278639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170    7.108271885 WTR  8      o*      O -0.8200
+H11      3.265271902    0.012384000    0.677304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    0.240624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    0.609695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    0.977183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040    6.958584023    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    0.045288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    0.680471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    0.608328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    0.776808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080    6.987744141    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    0.433007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834    7.023744106 WTR  8      o*      O -0.8200
+H11      3.261815929    0.039672000    0.588599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    0.059904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    0.654839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    0.975168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990    7.193879843    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    0.124992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123    7.096392059 WTR  8      o*      O -0.8200
+H11      3.188807917    0.012960000    0.819000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    0.139176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    0.735695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    1.294919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006    7.088184071    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    0.056159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984    6.358464003    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    0.539423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819    7.138728046 WTR  8      o*      O -0.8200
+H11      3.124296069    0.137015994    0.811223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    0.202175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    0.719496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    1.229760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070    7.096752119    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943    7.141032171 WTR  8      o*      O -0.8200
+H11      3.352391982    0.191015996    0.712007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    0.328680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    0.118223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074    6.558336210    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    0.547056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189    7.157231855 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    0.804456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    0.115200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Mon Dec  1 18:08:55 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    0.639863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    0.928439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053    7.034184122    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    0.033984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071    6.529679918    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    0.501767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149    7.132535791 WTR  8      o*      O -0.8200
+H11      3.196944022    0.108216003    0.712584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    0.271296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2arc/test/water8.arc.trueflags

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    7.743599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    8.160479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024    6.987024021    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    7.482672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873    7.105968189 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    7.962192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    7.497000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090   -0.593928194    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910   -0.694511890    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    0.095184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    7.632575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    8.034192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106    6.820991850    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    7.405056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958    7.154640198 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    7.962192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    7.426511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860   -0.439487886    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165   -0.325584126    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    0.183599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    7.712136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    8.069832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015    6.869520092    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    7.412472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016    7.140239954 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    7.947576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    7.255799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006   -0.457199907    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168   -0.257111835    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    0.181008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    7.634880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    7.904520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000    6.811992073    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    7.478639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170    7.108271885 WTR  8      o*      O -0.8200
+H11      3.265271902    7.212384000    7.877304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    7.440624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    7.809695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    8.177183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040    6.958584023    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    7.245288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    7.880471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    7.808328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    7.976808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080    6.987744141    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    7.633007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834    7.023744106 WTR  8      o*      O -0.8200
+H11      3.261815929    7.239672000    7.788599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    7.259904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    7.854839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    8.175168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990    7.193879843    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    7.324992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123    7.096392059 WTR  8      o*      O -0.8200
+H11      3.188807917    7.212960000    8.019000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    7.339176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    7.935695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    8.494919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006    7.088184071    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    7.256159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984    6.358464003    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    7.739423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819    7.138728046 WTR  8      o*      O -0.8200
+H11      3.124296069    7.337015994    8.011223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    7.402175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    7.919496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    8.429760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070    7.096752119    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943    7.141032171 WTR  8      o*      O -0.8200
+H11      3.352391982    7.391015996    7.912007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    7.528680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    7.318223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074    6.558336210    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    7.747056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189    7.157231855 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    8.004456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    7.315200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Mon Dec  1 18:52:12 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    7.839863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    8.128439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053    7.034184122    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    7.233984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071    6.529679918    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    7.701767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149    7.132535791 WTR  8      o*      O -0.8200
+H11      3.196944022    7.308216003    7.912584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    7.471296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2arc/test/water8.car

@@ -0,0 +1,39 @@
+!BIOSYM archive 3
+PBC=ON
+Water box from Eric Simon
+!DATE Fri Oct 24 16:37:49 1997
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000 (P1)
+O1      -1.872180000    7.165790000    0.418170000 WTR 1       o*      O  -0.820
+H11     -1.689520000    7.089730000    1.354690000 WTR 1       h*      H   0.410
+H12     -1.895920000    8.108520000    0.254080000 WTR 1       h*      H   0.410
+end
+O1       9.230430000    4.657060000    4.156260000 WTR 2       o*      O  -0.820
+H11      9.465440000    4.921460000    3.266830000 WTR 2       h*      H   0.410
+H12     10.059570000    4.393230000    4.555190000 WTR 2       h*      H   0.410
+end
+O1       1.214310000    4.380410000    0.134700000 WTR 3       o*      O  -0.820
+H11      1.244720000    5.289710000    0.432150000 WTR 3       h*      H   0.410
+H12      1.722010000    3.897490000    0.786810000 WTR 3       h*      H   0.410
+end
+O1       9.017600000    8.540120000    2.278390000 WTR 4       o*      O  -0.820
+H11      8.743110000    9.029940000    3.053600000 WTR 4       h*      H   0.410
+H12      8.492560000    7.740110000    2.301640000 WTR 4       h*      H   0.410
+end
+O1       7.534550000    6.982930000   -0.678410000 WTR 5       o*      O  -0.820
+H11      7.696430000    6.754540000   -1.593760000 WTR 5       h*      H   0.410
+H12      6.605560000    7.211690000   -0.648830000 WTR 5       h*      H   0.410
+end
+O1      11.381660000    7.514670000    4.106050000 WTR 6       o*      O  -0.820
+H11     10.830010000    7.598050000    3.328260000 WTR 6       h*      H   0.410
+H12     10.771400000    7.298260000    4.811020000 WTR 6       h*      H   0.410
+end
+O1      -1.981430000    8.779190000    6.557090000 WTR 7       o*      O  -0.820
+H11     -1.575590000    8.982500000    7.399820000 WTR 7       h*      H   0.410
+H12     -2.552830000    8.033270000    6.739640000 WTR 7       h*      H   0.410
+end
+O1       5.393330000   10.403880000    5.782890000 WTR 8       o*      O  -0.820
+H11      5.694370000    9.503500000    5.905020000 WTR 8       h*      H   0.410
+H12      6.018620000   10.784410000    5.166110000 WTR 8       h*      H   0.410
+end
+end
+

tools/lmp2arc/test/water8.pos

@@ -0,0 +1,303 @@
+ ITEM: NUMBER OF ATOMS
+ 24
+ ITEM: BOX BOUNDS
+ 0.E+0,  7.2000000000000002
+ 0.E+0,  7.2000000000000002
+ 0.E+0,  7.2000000000000002
+ ITEM: TIMESTEP
+ 10000
+ ITEM: ATOMS
+    24  2 0.38912 0.80204 0.04125    0    0    1
+    23  2 0.44443 0.97490 0.10586    0    0    1
+    22  1 0.39545 0.92669 0.98694    0    0    0
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+    20  2 0.39496 0.85650 0.72425    0    0    0
+    19  1 0.38210 0.96279 0.64193    0    0    0
+    18  2 0.02666 0.20907 0.56769    1    0    0
+    17  2 0.16830 0.06709 0.59983    1    0    0
+    16  1 0.08960 0.11180 0.49650    1    0    0
+    15  2 0.10789 0.21301 0.92288    0    0    0
+    14  2 0.24939 0.32700 0.80911    0    0    0
+    13  1 0.20235 0.19951 0.81891    0    0    0
+    12  2 0.53321 0.64824 0.31770    0    0    0
+    11  2 0.70021 0.76272 0.23808    0    0    0
+    10  1 0.56179 0.76532 0.24532    0    0    0
+     9  2 0.42969 0.97042 0.39011    0    0    0
+     8  2 0.32315 0.13340 0.41763    0    1    0
+     7  1 0.38574 0.07550 0.31033    0    1    0
+     6  2 0.95281 0.98408 0.26305    0   -1    0
+     5  2 0.96793 0.88950 0.44411    0   -1    0
+     4  1 0.88582 0.88256 0.32684    0   -1    0
+     3  2 0.20770 0.05294 0.06393    0    0    0
+     2  2 0.15575 0.12577 0.25027    0    0    0
+     1  1 0.08934 0.10802 0.13052    0    0    0
+ ITEM: TIMESTEP
+ 10100
+ ITEM: ATOMS
+    24  2 0.39323 0.79766 0.03146    0    0    1
+    23  2 0.45209 0.98330 0.10586    0    0    1
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+     4  1 0.86509 0.91751 0.31671    0   -1    0
+     3  2 0.20766 0.06898 0.06354    0    0    0
+     2  2 0.17517 0.13064 0.25597    0    0    0
+     1  1 0.10937 0.09752 0.14204    0    0    0
+ ITEM: TIMESTEP
+ 10200
+ ITEM: ATOMS
+    24  2 0.42369 0.79308 0.00775    0    0    1
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+     2  2 0.18549 0.11650 0.24641    0    0    0
+     1  1 0.10399 0.08168 0.13836    0    0    0
+ ITEM: TIMESTEP
+ 10300
+ ITEM: ATOMS
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+     2  2 0.16153 0.10521 0.25141    0    0    0
+     1  1 0.09875 0.06835 0.13754    0    0    0
+ ITEM: TIMESTEP
+ 10400
+ ITEM: ATOMS
+    24  2 0.43709 0.78600 0.99587    0    0    0
+    23  2 0.42300 0.96510 0.09451    0    0    1
+    22  1 0.38889 0.91136 0.97200    0    0    0
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+     9  2 0.45596 0.96647 0.34959    0    0    0
+     8  2 0.38861 0.13572 0.42199    0    1    0
+     7  1 0.40635 0.08468 0.29508    0    1    0
+     6  2 0.96412 0.97944 0.29245    0   -1    0
+     5  2 0.88914 0.97218 0.48087    0   -1    0
+     4  1 0.85893 0.91634 0.35526    0   -1    0
+     3  2 0.21588 0.05266 0.06663    0    0    0
+     2  2 0.13561 0.08974 0.26703    0    0    0
+     1  1 0.09688 0.04954 0.13853    0    0    0
+ ITEM: TIMESTEP
+ 10500
+ ITEM: ATOMS
+    24  2 0.43285 0.81794 0.00832    0    0    1
+    23  2 0.45303 0.00551 0.08175    0    1    1
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+     9  2 0.46641 0.97052 0.34666    0    0    0
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+     3  2 0.19956 0.05164 0.06132    0    0    0
+     2  2 0.16562 0.09549 0.26056    0    0    0
+     1  1 0.09409 0.06312 0.14608    0    0    0
+ ITEM: TIMESTEP
+ 10600
+ ITEM: ATOMS
+    24  2 0.46842 0.84060 0.01933    0    0    1
+    23  2 0.44289 0.00180 0.11375    0    1    1
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+     5  2 0.92340 0.88051 0.46726    0   -1    0
+     4  1 0.88808 0.86072 0.33778    0   -1    0
+     3  2 0.20183 0.04163 0.06302    0    0    0
+     2  2 0.14327 0.11197 0.25304    0    0    0
+     1  1 0.08757 0.05819 0.13483    0    0    0
+ ITEM: TIMESTEP
+ 10700
+ ITEM: ATOMS
+    24  2 0.46403 0.83721 0.02808    0    0    1
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+     2  2 0.15048 0.11937 0.26048    0    0    0
+     1  1 0.09470 0.08079 0.14259    0    0    0
+ ITEM: TIMESTEP
+ 10800
+ ITEM: ATOMS
+    24  2 0.43829 0.83478 0.04565    0    0    1
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+     6  2 0.94280 0.96383 0.24927    0   -1    0
+     5  2 0.96872 0.85484 0.42583    0   -1    0
+     4  1 0.88614 0.85566 0.31016    0   -1    0
+     3  2 0.21508 0.06340 0.07698    0    0    0
+     2  2 0.16379 0.12070 0.26013    0    0    0
+     1  1 0.09583 0.09370 0.14533    0    0    0
+ ITEM: TIMESTEP
+ 10900
+ ITEM: ATOMS
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+    15  2 0.05957 0.16085 0.90425    0    0    0
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+    13  1 0.15918 0.19075 0.81021    0    0    0
+    12  2 0.49247 0.67390 0.31620    0    0    0
+    11  2 0.67492 0.75321 0.26698    0    0    0
+    10  1 0.54640 0.78335 0.26049    0    0    0
+     9  2 0.47513 0.00452 0.38475    0    1    0
+     8  2 0.33152 0.13104 0.42921    0    1    0
+     7  1 0.39565 0.09686 0.31214    0    1    0
+     6  2 0.92514 0.97126 0.23534    0   -1    0
+     5  2 0.97774 0.85109 0.40573    0   -1    0
+     4  1 0.88970 0.84974 0.30326    0   -1    0
+     3  2 0.20329 0.07753 0.04698    0    0    0
+     2  2 0.17543 0.11090 0.25155    0    0    0
+     1  1 0.09930 0.08376 0.13445    0    0    0
+ ITEM: TIMESTEP
+ 11000
+ ITEM: ATOMS
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+    23  2 0.44402 0.01503 0.09897    0    1    1
+    22  1 0.38641 0.94761 0.99063    0    0    0
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+    20  2 0.46044 0.90690 0.72048    0    0    0
+    19  1 0.40035 0.00472 0.64553    0    1    0
+    18  2 0.02400 0.19289 0.55066    1    0    0
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+    12  2 0.52990 0.66868 0.30043    0    0    0
+    11  2 0.70798 0.76858 0.24274    0    0    0
+    10  1 0.56584 0.79089 0.24203    0    0    0
+     9  2 0.45730 0.97697 0.35010    0    0    0
+     8  2 0.36639 0.12895 0.43696    0    1    0
+     7  1 0.39521 0.08887 0.30904    0    1    0
+     6  2 0.98307 0.93887 0.26862    0   -1    0
+     5  2 0.95272 0.88685 0.44622    0   -1    0
+     4  1 0.89865 0.85232 0.31824    0   -1    0
+     3  2 0.19364 0.05406 0.05850    0    0    0
+     2  2 0.15436 0.11836 0.25908    0    0    0
+     1  1 0.09080 0.08423 0.14628    0    0    0

tools/lmp2arc/test/water8_unwrap.arc

@@ -0,0 +1,398 @@
+!BIOSYM archive 3
+PBC=ON
+Frame 0  Number of Picoseconds =     5.0000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.643248010    0.777744001    0.939744008 WTR  1      o*      O -0.8200
+H11      1.121400046    0.905544019    1.801944065 WTR  1      h*      H  0.4100
+H12      1.495439994    0.381167999    0.460295981 WTR  1      h*      H  0.4100
+end
+O1       6.377903795    6.354432106    2.353248096 WTR  2      o*      O -0.8200
+H11      6.969096136    6.404400158    3.197592044 WTR  2      h*      H  0.4100
+H12      6.860231924    7.085376120    1.893959928 WTR  2      h*      H  0.4100
+end
+O1       2.777328086    0.543599975    2.234376025 WTR  3      o*      O -0.8200
+H11      2.326680064    0.960479951    3.006935906 WTR  3      h*      H  0.4100
+H12      3.093768024   -0.212975979    2.808791900 WTR  3      h*      H  0.4100
+end
+O1       4.044887924    5.510304022    1.766304052 WTR  4      o*      O -0.8200
+H11      5.041511822    5.491583920    1.714175963 WTR  4      h*      H  0.4100
+H12      3.839111853    4.667327785    2.287439990 WTR  4      h*      H  0.4100
+end
+O1       1.456920040    1.436471951    5.896152020 WTR  5      o*      O -0.8200
+H11      1.795608044    2.354399943    5.825591898 WTR  5      h*      H  0.4100
+H12      0.776808017    1.533671987    6.644735956 WTR  5      h*      H  0.4100
+end
+O1       0.645119977    0.804960001    3.574799895 WTR  6      o*      O -0.8200
+H11      1.211760020    0.483047980    4.318775797 WTR  6      h*      H  0.4100
+H12      0.191952007    1.505303979    4.087368107 WTR  6      h*      H  0.4100
+end
+O1       2.751119900    6.932088089    4.621895885 WTR  7      o*      O -0.8200
+H11      2.843711901    6.166800213    5.214600134 WTR  7      h*      H  0.4100
+H12      2.705256057    7.482672000    5.459184122 WTR  7      h*      H  0.4100
+end
+O1       2.847239971    6.672167873   -0.094031811 WTR  8      o*      O -0.8200
+H11      3.199895954    7.019280052    0.762192017 WTR  8      h*      H  0.4100
+H12      2.801664090    5.774687862    0.297000012 WTR  8      h*      H  0.4100
+end
+end
+Frame 1  Number of Picoseconds =     5.0500
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.787464005    0.702144009    1.022687995 WTR  1      o*      O -0.8200
+H11      1.261224031    0.940608001    1.842984009 WTR  1      h*      H  0.4100
+H12      1.495152032    0.496656007    0.457487977 WTR  1      h*      H  0.4100
+end
+O1       6.228648090    6.606071806    2.280311966 WTR  2      o*      O -0.8200
+H11      6.579287910    6.505488110    3.152663970 WTR  2      h*      H  0.4100
+H12      6.906744003    7.295184001    2.001383901 WTR  2      h*      H  0.4100
+end
+O1       2.961720085    0.432575995    2.279663944 WTR  3      o*      O -0.8200
+H11      2.808215976    0.834192002    3.171672034 WTR  3      h*      H  0.4100
+H12      3.319776106   -0.379008150    2.693519998 WTR  3      h*      H  0.4100
+end
+O1       4.020191860    5.430168200    1.728504002 WTR  4      o*      O -0.8200
+H11      4.941431952    5.639471912    1.764144015 WTR  4      h*      H  0.4100
+H12      4.014575958    4.480128050    1.745208049 WTR  4      h*      H  0.4100
+end
+O1       1.246895993    1.396152020    5.866631842 WTR  5      o*      O -0.8200
+H11      1.592640030    2.332368064    5.899392128 WTR  5      h*      H  0.4100
+H12      0.572184008    1.531511950    6.572448063 WTR  5      h*      H  0.4100
+end
+O1       0.712511981    0.765359974    3.554783964 WTR  6      o*      O -0.8200
+H11      1.439495981    0.479375982    4.145327854 WTR  6      h*      H  0.4100
+H12      0.433296007    1.464119947    4.176144075 WTR  6      h*      H  0.4100
+end
+O1       2.728656077    6.963191843    4.645943928 WTR  7      o*      O -0.8200
+H11      3.408552074    6.317351961    5.011056089 WTR  7      h*      H  0.4100
+H12      2.620007944    7.405056006    5.514840174 WTR  7      h*      H  0.4100
+end
+O1       2.781791925    6.725951958   -0.045359802 WTR  8      o*      O -0.8200
+H11      3.255047965    7.079759789    0.762192017 WTR  8      h*      H  0.4100
+H12      2.831255937    5.743151951    0.226511988 WTR  8      h*      H  0.4100
+end
+end
+Frame 2  Number of Picoseconds =     5.1000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.748728025    0.588095999    0.996191955 WTR  1      o*      O -0.8200
+H11      1.335527980    0.838799983    1.774151981 WTR  1      h*      H  0.4100
+H12      1.458215976    0.362951991    0.341352001 WTR  1      h*      H  0.4100
+end
+O1       6.050879860    6.760512114    2.297663927 WTR  2      o*      O -0.8200
+H11      6.377544165    6.874415874    3.235032034 WTR  2      h*      H  0.4100
+H12      6.719327974    7.383599997    1.901664090 WTR  2      h*      H  0.4100
+end
+O1       2.932199907    0.512136000    2.235168028 WTR  3      o*      O -0.8200
+H11      2.719512105    0.869832015    3.124511933 WTR  3      h*      H  0.4100
+H12      3.350520015   -0.330479908    2.583936095 WTR  3      h*      H  0.4100
+end
+O1       3.985632133    5.410440016    1.812528062 WTR  4      o*      O -0.8200
+H11      4.970664167    5.586623812    1.901016068 WTR  4      h*      H  0.4100
+H12      4.033223963    4.442111921    2.060784101 WTR  4      h*      H  0.4100
+end
+O1       1.344383991    1.367640030    5.875344086 WTR  5      o*      O -0.8200
+H11      1.556711948    2.309399986    5.813136148 WTR  5      h*      H  0.4100
+H12      0.630144024    1.341864002    6.548687983 WTR  5      h*      H  0.4100
+end
+O1       0.732240003    0.728207999    3.522168088 WTR  6      o*      O -0.8200
+H11      1.093391991    0.133343996    4.209912014 WTR  6      h*      H  0.4100
+H12      0.568655992    1.451015961    4.075056124 WTR  6      h*      H  0.4100
+end
+O1       2.891015983    7.045991850    4.660992193 WTR  7      o*      O -0.8200
+H11      3.343967915    6.323039961    5.084495831 WTR  7      h*      H  0.4100
+H12      2.646215916    7.412472005    5.564231873 WTR  7      h*      H  0.4100
+end
+O1       2.803895903    6.645096016   -0.059760046 WTR  8      o*      O -0.8200
+H11      3.289896083    6.875423956    0.747576016 WTR  8      h*      H  0.4100
+H12      3.050567937    5.710175800    0.055799999 WTR  8      h*      H  0.4100
+end
+end
+Frame 3  Number of Picoseconds =     5.1500
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.711000019    0.492120016    0.990287983 WTR  1      o*      O -0.8200
+H11      1.163016021    0.757511991    1.810152054 WTR  1      h*      H  0.4100
+H12      1.601927984    0.311904001    0.531359982 WTR  1      h*      H  0.4100
+end
+O1       6.059520006    6.742800093    2.409191895 WTR  2      o*      O -0.8200
+H11      6.539976168    6.942888165    3.208751965 WTR  2      h*      H  0.4100
+H12      6.548400021    7.381008004    1.913111973 WTR  2      h*      H  0.4100
+end
+O1       2.851128101    0.434880012    2.226743960 WTR  3      o*      O -0.8200
+H11      2.793240023    0.704520017    3.184920001 WTR  3      h*      H  0.4100
+H12      3.311640000   -0.388007927    2.550096059 WTR  3      h*      H  0.4100
+end
+O1       4.017023849    5.447736025    1.724400008 WTR  4      o*      O -0.8200
+H11      5.052887821    5.477760029    1.815192032 WTR  4      h*      H  0.4100
+H12      3.806496191    4.653288031    2.253816032 WTR  4      h*      H  0.4100
+end
+O1       1.276776016    1.276056004    5.882616091 WTR  5      o*      O -0.8200
+H11      1.311047995    2.248991919    5.986656189 WTR  5      h*      H  0.4100
+H12      0.596375978    1.036727965    6.544511890 WTR  5      h*      H  0.4100
+end
+O1       0.691128016    0.825624007    3.500711918 WTR  6      o*      O -0.8200
+H11      1.160279953    0.358919987    4.233024073 WTR  6      h*      H  0.4100
+H12      0.559367985    1.739880002    3.949127913 WTR  6      h*      H  0.4100
+end
+O1       2.977559924    7.081775951    4.662864161 WTR  7      o*      O -0.8200
+H11      3.621240091    6.645456076    5.265287876 WTR  7      h*      H  0.4100
+H12      2.522519946    7.478639996    5.415695858 WTR  7      h*      H  0.4100
+end
+O1       2.913336039    6.708096170   -0.091728115 WTR  8      o*      O -0.8200
+H11      3.265271902    7.212384000    0.677304018 WTR  8      h*      H  0.4100
+H12      3.154823899    5.800824165    0.240624002 WTR  8      h*      H  0.4100
+end
+end
+Frame 4  Number of Picoseconds =     5.2000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.697535974    0.356687987    0.997416008 WTR  1      o*      O -0.8200
+H11      0.976391995    0.646128005    1.922616005 WTR  1      h*      H  0.4100
+H12      1.554336047    0.379151997    0.479735988 WTR  1      h*      H  0.4100
+end
+O1       6.184295940    6.597647953    2.557872105 WTR  2      o*      O -0.8200
+H11      6.401808071    6.999696064    3.462264061 WTR  2      h*      H  0.4100
+H12      6.941663790    7.051967812    2.105640078 WTR  2      h*      H  0.4100
+end
+O1       2.925719905    0.609695989    2.124576044 WTR  3      o*      O -0.8200
+H11      2.797992039    0.977183998    3.038328052 WTR  3      h*      H  0.4100
+H12      3.282912040   -0.241415977    2.517048025 WTR  3      h*      H  0.4100
+end
+O1       4.028759909    5.573880100    1.824696064 WTR  4      o*      O -0.8200
+H11      4.974191809    5.553863955    1.971648073 WTR  4      h*      H  0.4100
+H12      3.791735888    4.679711866    2.177279949 WTR  4      h*      H  0.4100
+end
+O1       1.227888036    1.316304052    5.946911860 WTR  5      o*      O -0.8200
+H11      1.263024008    2.294928074    6.034680176 WTR  5      h*      H  0.4100
+H12      0.600192010    1.193327987    6.723647833 WTR  5      h*      H  0.4100
+end
+O1       0.782856023    0.856223989    3.495383978 WTR  6      o*      O -0.8200
+H11      1.577015948    0.427895996    3.934583902 WTR  6      h*      H  0.4100
+H12      0.643176019    1.503216040    4.174560070 WTR  6      h*      H  0.4100
+end
+O1       2.846591949    7.148952198    4.558031845 WTR  7      o*      O -0.8200
+H11      3.674304056    6.851015854    4.966343880 WTR  7      h*      H  0.4100
+H12      2.399040055    7.245288000    5.449895954 WTR  7      h*      H  0.4100
+end
+O1       2.800007987    6.561792183    6.998400021 WTR  8      o*      O -0.8200
+H11      3.045600057    6.948719931    7.880471975 WTR  8      h*      H  0.4100
+H12      3.147048068    5.659200096    7.170263958 WTR  8      h*      H  0.4100
+end
+end
+Frame 5  Number of Picoseconds =     5.2500
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.677447999    0.454464000    1.051776016 WTR  1      o*      O -0.8200
+H11      1.192463994    0.687528008    1.876032043 WTR  1      h*      H  0.4100
+H12      1.436832011    0.371808001    0.441503996 WTR  1      h*      H  0.4100
+end
+O1       6.311375999    6.377472067    2.554200053 WTR  2      o*      O -0.8200
+H11      6.487559795    6.340536118    3.495959902 WTR  2      h*      H  0.4100
+H12      7.071120071    6.984288168    2.246183968 WTR  2      h*      H  0.4100
+end
+O1       2.910095930    0.608328009    2.146032000 WTR  3      o*      O -0.8200
+H11      2.564928031    0.776808017    3.064392042 WTR  3      h*      H  0.4100
+H12      3.358152080   -0.212255859    2.495951915 WTR  3      h*      H  0.4100
+end
+O1       3.981959867    5.584248018    1.721880019 WTR  4      o*      O -0.8200
+H11      4.950287962    5.821992159    1.943856096 WTR  4      h*      H  0.4100
+H12      4.066415977    4.644144058    1.999728012 WTR  4      h*      H  0.4100
+end
+O1       1.139759982    1.205783951    5.937767887 WTR  5      o*      O -0.8200
+H11      1.104983962    2.151792097    6.154271936 WTR  5      h*      H  0.4100
+H12      0.647712010    0.816407990    6.680592155 WTR  5      h*      H  0.4100
+end
+O1       0.784080023    0.831672013    3.501144075 WTR  6      o*      O -0.8200
+H11      1.266048038    0.577151996    4.329144144 WTR  6      h*      H  0.4100
+H12      0.142416005    1.515167964    3.979296112 WTR  6      h*      H  0.4100
+end
+O1       2.891736102    7.193015957    4.560623932 WTR  7      o*      O -0.8200
+H11      3.187727952    6.321167994    4.886351824 WTR  7      h*      H  0.4100
+H12      2.786687922    7.633007991    5.464296198 WTR  7      h*      H  0.4100
+end
+O1       2.824127913    6.804863834   -0.176255894 WTR  8      o*      O -0.8200
+H11      3.261815929    7.239672000    0.588599986 WTR  8      h*      H  0.4100
+H12      3.116520023    5.889167976    0.059904000 WTR  8      h*      H  0.4100
+end
+end
+Frame 6  Number of Picoseconds =     5.3000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.630503976    0.418967995    0.970775986 WTR  1      o*      O -0.8200
+H11      1.031544006    0.806184000    1.821887898 WTR  1      h*      H  0.4100
+H12      1.453175998    0.299735999    0.453743988 WTR  1      h*      H  0.4100
+end
+O1       6.394176006    6.197183847    2.432015991 WTR  2      o*      O -0.8200
+H11      6.648479891    6.339671803    3.364272022 WTR  2      h*      H  0.4100
+H12      7.104600048    6.844679832    2.257199907 WTR  2      h*      H  0.4100
+end
+O1       2.814191937    0.654839981    2.191392016 WTR  3      o*      O -0.8200
+H11      2.293992090    0.975168049    2.990375948 WTR  3      h*      H  0.4100
+H12      3.366143990   -0.006120157    2.763432097 WTR  3      h*      H  0.4100
+end
+O1       3.949055815    5.635655880    1.773792028 WTR  4      o*      O -0.8200
+H11      4.936967897    5.687280035    1.804176092 WTR  4      h*      H  0.4100
+H12      3.832056141    4.710311794    2.078568006 WTR  4      h*      H  0.4100
+end
+O1       1.225584018    1.349136007    5.889312172 WTR  5      o*      O -0.8200
+H11      1.484784007    2.321855950    5.976575804 WTR  5      h*      H  0.4100
+H12      0.578447986    1.216584027    6.641855907 WTR  5      h*      H  0.4100
+end
+O1       0.668376017    0.703008002    3.512016034 WTR  6      o*      O -0.8200
+H11      1.214784050    0.428472000    4.290335798 WTR  6      h*      H  0.4100
+H12      0.152568005    1.261224031    4.095143938 WTR  6      h*      H  0.4100
+end
+O1       2.910960031    7.140600014    4.607999897 WTR  7      o*      O -0.8200
+H11      3.731039858    7.014095879    5.183928108 WTR  7      h*      H  0.4100
+H12      2.376503921    7.324992000    5.400360060 WTR  7      h*      H  0.4100
+end
+O1       2.919960022    6.901776123   -0.103607941 WTR  8      o*      O -0.8200
+H11      3.188807917    7.212960000    0.819000024 WTR  8      h*      H  0.4100
+H12      3.372623992    6.052320099    0.139176004 WTR  8      h*      H  0.4100
+end
+end
+Frame 7  Number of Picoseconds =     5.3500
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.681840008    0.581687987    1.026648009 WTR  1      o*      O -0.8200
+H11      1.083456016    0.859463990    1.875455904 WTR  1      h*      H  0.4100
+H12      1.559448016    0.402767989    0.594576001 WTR  1      h*      H  0.4100
+end
+O1       6.323832178    6.073488092    2.298023987 WTR  2      o*      O -0.8200
+H11      6.825743866    6.188615799    3.118967915 WTR  2      h*      H  0.4100
+H12      6.738839865    6.851592207    1.866096067 WTR  2      h*      H  0.4100
+end
+O1       2.858544087    0.735695976    2.211984086 WTR  3      o*      O -0.8200
+H11      2.780351901    1.294919980    3.005999923 WTR  3      h*      H  0.4100
+H12      3.192192006   -0.111815929    2.615255928 WTR  3      h*      H  0.4100
+end
+O1       3.902903795    5.665679884    1.852632022 WTR  4      o*      O -0.8200
+H11      4.888943911    5.545152140    1.843919992 WTR  4      h*      H  0.4100
+H12      3.620447874    4.914503860    2.399544096 WTR  4      h*      H  0.4100
+end
+O1       1.187567997    1.361880040    5.822135925 WTR  5      o*      O -0.8200
+H11      1.158335996    2.323151994    6.054335833 WTR  5      h*      H  0.4100
+H12      0.511055982    1.029311979    6.455015802 WTR  5      h*      H  0.4100
+end
+O1       0.714959979    0.448776001    3.522168088 WTR  6      o*      O -0.8200
+H11      1.522439969    0.256248003    4.049639940 WTR  6      h*      H  0.4100
+H12      0.399744013    1.145736051    4.144967794 WTR  6      h*      H  0.4100
+end
+O1       2.987207937    0.056159998    4.631472015 WTR  7      o*      O -0.8200
+H11      2.966543984   -0.841535997    5.050224066 WTR  7      h*      H  0.4100
+H12      2.724192023    0.539423990    5.513111973 WTR  7      h*      H  0.4100
+end
+O1       2.876688051    6.898391819   -0.061271954 WTR  8      o*      O -0.8200
+H11      3.124296069    7.337015994    0.811223978 WTR  8      h*      H  0.4100
+H12      3.341015983    6.027911997    0.202175997 WTR  8      h*      H  0.4100
+end
+end
+Frame 8  Number of Picoseconds =     5.4000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.689976007    0.674639994    1.046375978 WTR  1      o*      O -0.8200
+H11      1.179288018    0.869040012    1.872935915 WTR  1      h*      H  0.4100
+H12      1.548575950    0.456480002    0.554256016 WTR  1      h*      H  0.4100
+end
+O1       6.380207920    6.160752153    2.233152080 WTR  2      o*      O -0.8200
+H11      6.974784136    6.154847860    3.065976048 WTR  2      h*      H  0.4100
+H12      6.788159895    6.939575958    1.794744051 WTR  2      h*      H  0.4100
+end
+O1       2.898792028    0.719496024    2.252736068 WTR  3      o*      O -0.8200
+H11      2.751984000    1.229760003    3.074615979 WTR  3      h*      H  0.4100
+H12      3.222576070   -0.103247881    2.715407896 WTR  3      h*      H  0.4100
+end
+O1       3.914711952    5.619239902    1.807055926 WTR  4      o*      O -0.8200
+H11      4.942224169    5.491295958    1.859687948 WTR  4      h*      H  0.4100
+H12      3.487895894    4.802327871    2.186423922 WTR  4      h*      H  0.4100
+end
+O1       1.031759977    1.262375987    5.822208023 WTR  5      o*      O -0.8200
+H11      0.922895980    2.229624009    6.004151917 WTR  5      h*      H  0.4100
+H12      0.580823994    0.948239958    6.654672146 WTR  5      h*      H  0.4100
+end
+O1       0.724319977    0.401832005    3.522239971 WTR  6      o*      O -0.8200
+H11      1.466999996    0.287999994    4.135752153 WTR  6      h*      H  0.4100
+H12      0.175104006    1.018584001    4.138775969 WTR  6      h*      H  0.4100
+end
+O1       2.921975970    0.058031999    4.665167856 WTR  7      o*      O -0.8200
+H11      3.729743814    0.090144002    5.195159912 WTR  7      h*      H  0.4100
+H12      2.418047905    0.066024003    5.525711918 WTR  7      h*      H  0.4100
+end
+O1       2.955384064    6.917759943   -0.058967829 WTR  8      o*      O -0.8200
+H11      3.352391982    7.391015996    0.712007993 WTR  8      h*      H  0.4100
+H12      3.155688000    6.010415840    0.328680012 WTR  8      h*      H  0.4100
+end
+end
+Frame 9  Number of Picoseconds =     5.4500
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.714959979    0.603072006    0.968040025 WTR  1      o*      O -0.8200
+H11      1.263095999    0.798479998    1.811159921 WTR  1      h*      H  0.4100
+H12      1.463688004    0.558215976    0.338256007 WTR  1      h*      H  0.4100
+end
+O1       6.405839968    6.118128204    2.183471990 WTR  2      o*      O -0.8200
+H11      7.039727926    6.127848101    2.921256065 WTR  2      h*      H  0.4100
+H12      6.661008167    6.993072081    1.694447994 WTR  2      h*      H  0.4100
+end
+O1       2.848679996    0.697391993    2.247407913 WTR  3      o*      O -0.8200
+H11      2.386943936    0.943488050    3.090312052 WTR  3      h*      H  0.4100
+H12      3.420935941    0.032544000    2.770200062 WTR  3      h*      H  0.4100
+end
+O1       3.934080076    5.640119934    1.875528002 WTR  4      o*      O -0.8200
+H11      4.859424162    5.423112059    1.922255945 WTR  4      h*      H  0.4100
+H12      3.545783973    4.852080059    2.276639915 WTR  4      h*      H  0.4100
+end
+O1       1.146096003    1.373400021    5.833511925 WTR  5      o*      O -0.8200
+H11      1.009799981    2.354903984    5.825519800 WTR  5      h*      H  0.4100
+H12      0.428903997    1.158120024    6.510600185 WTR  5      h*      H  0.4100
+end
+O1       0.727559978    0.398736012    3.565944099 WTR  6      o*      O -0.8200
+H11      1.207295966    0.319319987    4.473647833 WTR  6      h*      H  0.4100
+H12      0.138815998    1.068048012    3.947400141 WTR  6      h*      H  0.4100
+end
+O1       2.980800033    0.118223995    4.698504066 WTR  7      o*      O -0.8200
+H11      3.425616074   -0.641663790    5.115167856 WTR  7      h*      H  0.4100
+H12      2.681639957    0.547056001    5.574168062 WTR  7      h*      H  0.4100
+end
+O1       2.820600057    6.892344189   -0.042768145 WTR  8      o*      O -0.8200
+H11      3.277007961    7.011792183    0.804456013 WTR  8      h*      H  0.4100
+H12      2.911608052    5.904360008    0.115200005 WTR  8      h*      H  0.4100
+end
+end
+Frame 10  Number of Picoseconds =     5.5000
+!DATE Mon Dec  1 18:10:28 2003
+PBC    7.2000    7.2000    7.2000   90.0000   90.0000   90.0000  (P1)
+O1       0.653760016    0.606455988    1.053216040 WTR  1      o*      O -0.8200
+H11      1.111391973    0.852191985    1.865375948 WTR  1      h*      H  0.4100
+H12      1.394207954    0.389232007    0.421199995 WTR  1      h*      H  0.4100
+end
+O1       6.470279932    6.136704111    2.291327906 WTR  2      o*      O -0.8200
+H11      6.859583902    6.385319996    3.212784076 WTR  2      h*      H  0.4100
+H12      7.078104115    6.759864092    1.934064102 WTR  2      h*      H  0.4100
+end
+O1       2.845511985    0.639863974    2.225088072 WTR  3      o*      O -0.8200
+H11      2.638007927    0.928439999    3.146112084 WTR  3      h*      H  0.4100
+H12      3.292560053   -0.165815878    2.520720077 WTR  3      h*      H  0.4100
+end
+O1       4.074048042    5.694407845    1.742615962 WTR  4      o*      O -0.8200
+H11      5.097455835    5.533776140    1.747728038 WTR  4      h*      H  0.4100
+H12      3.815280104    4.814496088    2.163095999 WTR  4      h*      H  0.4100
+end
+O1       1.124495959    1.296288013    5.887223911 WTR  5      o*      O -0.8200
+H11      1.304711974    2.253239894    5.959152174 WTR  5      h*      H  0.4100
+H12      0.454032004    1.074528015    6.563952112 WTR  5      h*      H  0.4100
+end
+O1       0.697103977    0.596160007    3.525839925 WTR  6      o*      O -0.8200
+H11      1.223784041    0.430272004    4.395599842 WTR  6      h*      H  0.4100
+H12      0.172800002    1.388808024    3.964752102 WTR  6      h*      H  0.4100
+end
+O1       2.882520032    0.033984001    4.647815895 WTR  7      o*      O -0.8200
+H11      3.315168071   -0.670320082    5.187456179 WTR  7      h*      H  0.4100
+H12      2.643839908    0.501767975    5.504255962 WTR  7      h*      H  0.4100
+end
+O1       2.782151985    6.822792149   -0.067464209 WTR  8      o*      O -0.8200
+H11      3.196944022    7.308216003    0.712584025 WTR  8      h*      H  0.4100
+H12      2.898863912    5.900328112    0.271296000 WTR  8      h*      H  0.4100
+end
+end

tools/lmp2cfg/README.txt

@@ -0,0 +1,66 @@
+README.txt
+
+lmp2cfg
+
+Version 1.0
+Ara Kooser
+8/1/04
+
+Contents
+I.   Before you start
+II.  Introduction
+III. Compiling the program
+IV.  Running the program
+
+
+I. Before you start
+
+1) Read the READMEFIRST file
+2) You will need either f77 or g77 compiler
+3) A text editor (VI or emacs)
+4) AtomEye( http://164.107.79.177/Archive/Graphics/A/) good as of 8/1/04
+5) A sense of adventure and humor
+
+
+II. Introduction
+
+The lmp2cfg program converts a LAMMPS atom dump file into a series of .cfg
+files.(000001.cfg, 000002.cfg,...). These files can be read into AtomEye
+and made into a movie or viewed indivdually.
+
+
+III. Compiling the program
+
+The program should comply with either command f77 lmp2cfg.f or
+g77 lmp2cfg.f
+
+IV. Running the program
+
+You need to create a user input file. In the examples folder you will find
+an example input script, LAMMPS dump file, and the correct .cfg output. 
+The input script reads like this:
+
+7              #number of atom types in your LAMMPS file       
+'dump.atom'    #name of the LAMMPS dump file, you need the ' '
+1              #first frame
+10             #last frame
+1              #first atom type
+26.98154       #atomic weight
+'ao'           #atom name
+2              #second atom type
+15.9994        #atomic weight
+'oh'           #atom name
+ 
+
+Make sure the input file and the atom dump file are in the same folder.
+On the command line type
+
+lmp2cfg < input_file.txt > out
+
+You should get several .cfg files. For reading into AtomEye and making
+movies see the AtomEye homepage.
+
+
+
+
+

tools/lmp2cfg/examples/lmp2cfg_inp.txt

@@ -0,0 +1,25 @@
+7
+'dump.atom'
+1
+3
+1
+26.98154
+'ao'
+2
+15.9994
+'oh'
+3
+1.00794
+'ho'
+4
+15.9994
+'o*'
+5
+1.00794
+'h*'
+6
+35.4527
+'Cl'
+7
+207.2
+'Pb'

tools/lmp2cfg/lmp2cfg.f

@@ -0,0 +1,185 @@
+*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12
+c----------------------------------------------------------------------
+      program lammps to cfg
+c----------------------------------------------------------------------
+*Programming by Jeff Greathouse and Ara Kooser
+*Version 1.0 9/1/04
+*Sandia National Labs
+*Converts LAMMPS atom dump to .cfg files for AtomEye
+*This program is provided as is. Please see the README file.
+c----------------------------------------------------------------------
+      implicit real*8 (a-h,o-z)
+      
+      character*12 inhist,snapshot
+      character*4 fftype(100),name,ciframe
+
+      integer natom,iatom,itype(50000),q
+      integer atype(99),itycon,ntype,mass(99)
+
+      dimension x(50000),y(50000),z(50000)
+      dimension amass(99)
+
+
+c-------Reads in the user input file-------------------------------
+
+          read(*,*) ntype
+          read(*,*) inhist
+          read(*,*) iframe1
+          read(*,*) iframe2
+c          write(*,*) ntype
+c          write(*,*) inhist
+       do 1, i=1, ntype
+
+          read(*,*) atype(i)
+          read(*,*) amass(i)
+          mass(i)=anint(amass(i))  
+          read(*,*) fftype(i)
+
+       
+c          write(*,*) atype(i)
+c          write(*,*) amass(i)
+c          write(*,*) fftype(i)
+ 1     continue
+
+c-------Lammps output file is 9, reads in lmps header--------------         
+
+         name=inhist(1:4)
+         open(9,file=inhist,status='old',form='formatted',err=999)
+c         open(2,status='new',form='formatted')
+
+
+          iatom=0
+          iframe=0
+          jframe=0
+
+c---------------------------------------------------------------------
+c----------This begins the frame by frame reading section-------------
+
+ 9999    continue
+
+         read(9,*,end=999)
+         read(9,*,end=999)
+         read(9,*,end=999)
+         read(9,*,end=999) natom
+         read(9,*,end=999)
+         read(9,50,end=999) xcell
+         read(9,50,end=999) ycell
+         read(9,50,end=999) zcell
+         read(9,*,end=999)
+
+ 50      format(2x,f12.5)
+
+
+
+ 1000    format(1x,i5,1x,i2,3f9.5)
+         
+
+
+
+
+ 
+
+         do 440 j=1,natom
+ 420      read(9,*,end=999)iatom,itype(iatom),x(iatom),y(iatom),z(iatom)
+
+
+*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12 
+
+
+ 
+
+ 440      continue
+
+          jframe=jframe+1
+          if(jframe.lt.iframe1)goto 9999
+          iframe=iframe+1
+      
+          if(iframe.ge.iframe2) goto 999
+          
+
+c--------------------------------------------------------------------
+c-------This section writes each ts to a seperate .cfg file----------
+
+c         ciframe=char(iframe)
+c         snapshot(iframe)=name//ciframe//'.cfg'
+c         write(*,*)ciframe
+         
+c         write(snapshot,'("Cfgs/",i7.7,".cfg")') iframe
+         ciframe='.cfg'
+c         write(*,*)ciframe 
+         write(snapshot,'(i5.5,a4)')iframe,ciframe
+c         write(*,*)snapshot
+         open(unit=iframe+20,file=snapshot,status='new',
+     *   form='formatted',err=999)
+
+          write((iframe+20),'(a22,i7)')'Number of particles = ',natom
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a16)')'A = 1.5 Angstrom'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),435)'H0(1,1) = ',xcell,' A'
+          write((iframe+20),'(a14)')'H0(1,2) = 0 A'
+          write((iframe+20),'(a14)')'H0(1,3) = 0 A'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a14)')'H0(2,1) = 0 A'
+          write((iframe+20),435)'H0(2,2) = ',ycell,' A'
+          write((iframe+20),'(a14)')'H0(2,3) = 0 A'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a14)')'H0(3,1) = 0 A'
+          write((iframe+20),'(a14)')'H0(3,2) = 0 A'
+          write((iframe+20),435)'H0(3,3) = ',zcell,' A'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a12)')'eta(1,1) = 0'
+          write((iframe+20),'(a12)')'eta(1,2) = 0'
+          write((iframe+20),'(a12)')'eta(1,3) = 0'
+          write((iframe+20),'(a12)')'eta(2,2) = 0'
+          write((iframe+20),'(a12)')'eta(2,3) = 0'
+          write((iframe+20),'(a12)')'eta(3,3) = 0'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),*)
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          write((iframe+20),'(a1)')'#'
+          
+ 435      format(a11,f10.5,a2)
+
+          do 460, j=1,natom
+          
+           do 450,i=1,ntype
+c            write(*,*)i,amass(i),fftype(i) 
+c             write(*,*)ntype
+            if(itype(j).eq.atype(i))
+     *        write((iframe+20),445)mass(i),fftype(i),x(j),
+     *      y(j),z(j),' 0',' 0',' 0'
+
+c---445 is the format for writing atom data to .cfg file------------
+ 445     format(i3.3,1x,a2,1x,3f9.6,3a2)
+
+ 450      continue
+
+ 460      continue
+
+          go to 9999
+
+ 999      continue
+            close(9)      
+
+
+
+ 200     continue   
+
+         stop
+           end

tools/lmp2traj/README.txt

@@ -0,0 +1,78 @@
+README.txt
+
+lmp2traj
+
+Version 1.0
+Ara Kooser
+8/1/04
+
+Contents
+I.   Before you start
+II.  Introduction
+III. Compiling the program
+IV.  Running the program
+
+I. Before you start
+
+1) Read the READMEFIRST file
+2) You will need either f77 or g77 compiler
+3) A text editor (VI or emacs)
+4) LAMMPS
+5) A graphing program that can do contours
+6) A sense of adventure and humor
+
+II. Introduction
+
+This program will take a LAMMPS atom dump file and provide the following three
+files.
+1) data for making contour maps
+2) density profile
+3) dipole information
+
+III. Compiling the program
+
+To compile the program run either ./f77 lmp2traj.f or
+./g77 traj.f
+
+IV. Running the program
+
+First you need to create a user input file. There is an example of an input file
+in the examples folder.
+
+The input file reads like this:
+
+'atom'                        # dump file name, needs the ' '
+1                             # first frame
+60                            # last frame
+38.26119                      # x dimension of the box
+44.26119                      # y dimension of the box
+48.33150                      # z dimension of the box
+90.                           # angles of the box, always 90
+90.                           # angles of the box, always 90                      
+90.                           # angles of the box, always 90
+82844.6                       # volumne of the box in cubic Angstroms
+5                             # water oxygen atom type from LAMMPS (#)
+6                             # water hydrogen atom type from LAMMPS(#)
+0.                            # leave at 0 
+5.                            # number of atom types
+0.                            # z shift leave at 0
+5.                            # number of density maps
+'Surface (1) ho'              # Enter name/description of atom
+2                             # atom type number from LAMMPS
+'ho'                          # Column name for data
+0                             # Defines inner sphere, in A
+48.3                          # Defines out sphere, in A
+
+
+Make sure you have the input file and the LAMMPS atom dump file in the same
+directory.
+
+To run the program type
+   lmp2traj < inp_file.txt > out
+
+This should give you three files like in the examples/output folder. 
+
+
+
+
+

tools/lmp2traj/examples/lmp2traj_inp.txt

@@ -0,0 +1,26 @@
+'dump.atom'
+1
+3
+29.00000
+38.26120
+44.79980
+90.
+90.
+90.
+49708.7291
+1
+2
+0.
+2.
+0.
+2
+'Bulk (1) O-water'
+1
+'o*'
+18.6
+21.0
+'Bulk (1) H-water'
+2
+'h*'
+18.1
+21.5

tools/lmp2traj/lmp2traj.f

@@ -0,0 +1,449 @@
+*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12
+*********************************************************************
+      program densprof 
+
+*********************************************************************
+*** Density profile calculations for orthogonal cells
+***
+***  modified for more atom types (up to 20) and with generalized 
+***  surface map arrays - 1 array 40x50x50 for 20 atom types x2 surfaces
+***  A.K. 8-13-02
+*** Modified for reading in the x direction Ara Kooser
+*** Modified for reading in LAMMPS files Jeff Greathouse and Ara Kooser
+*** 7/19/04
+*********************************************************************
+
+      implicit real*8 (a-h,o-z)
+
+      LOGICAL       exists
+
+      character*12 inhist,outout,outeang,outhb,
+     *    outsurf,outacf,outdat,outang
+      character name*4,file*10,text*6
+      character*5 mapat(20),rtype
+      character*8 colname(40)
+      character*40 mapcom(40)
+      character dummy*18, dummy1*12, dummy2*100
+
+      integer natom, ntype, nmaps, iconn(12), ndip(1000), mapid(20)
+      integer otype, htype, atype(1000)
+      integer itype(50000), icount(50), iwato(50000), iwath(50000,2)
+
+      dimension  x(50000),y(50000),z(50000),q(50000)
+      dimension  g(50,1000),dipx(1000),dipy(1000),dipz(1000),dip(1000)
+      dimension  dipa(1000),dipc(1000),angdis(60,100)
+      dimension  smap(40,50,50)
+      dimension  amapmin(40),amapmax(40),amamap(40),psmap(40)
+
+
+
+      dummy1='123456789|123'
+
+c************************************
+      read (*,*) inhist
+      read (*,*) iframe1
+      read (*,*) iframe2
+      read (*,*) acell
+      read (*,*) bcell
+      read (*,*) ccell
+      read (*,*) alpha
+      read (*,*) beta
+      read (*,*) gamma
+      read (*,*) vol
+      read (*,*) otype
+      read (*,*) htype
+      read (*,*) watmiz
+      read (*,*) watmaz
+      read (*,*) zshift
+      read (*,*) nmaps
+      do 1 i=1,nmaps
+         read (*,*) mapcom(i)
+         read (*,*) mapid(i)
+         read (*,*) colname(i)
+         read (*,*) amapmin(i)
+         read (*,*) amapmax(i)
+  1   continue
+**************************************
+c      write(*,*) (mapcom(i),mapid(i),colname(i),amapmin(i),
+c     *            amapmax(i),i=1,nmaps)
+      name=inhist(1:4)
+      outout=name//'-out.txt'
+      outsurf=name//'-srf.txt'
+      outdat=name//'-dat.bin'
+      outang=name//'-ang.txt'
+      open(11,file=outout,status='new',form='formatted',err=999)
+      open(12,file=outsurf,status='new',form='formatted',err=999)
+      open(13,file=outang,status='new',form='formatted',err=999)
+      write(11,'(a35,a15)') 'Analysis output file - ', outout
+c---- removed     
+      write(11,'(a35,a15)') 'Input trajectory (*.asc) - ', inhist
+      write(11,'(a35,i7)') 'First frame to analyze - ', iframe1
+      write(11,'(a35,i7)') 'Total frames to analyze - ', iframe2 
+      write(11,'(a35,i7)') 'Total number of atoms - ', natom
+      write(11,'(a35,i7)') 'Total number of atom types - ', ntype
+      if(nwat.ne.(iwat-1)) write(*,*) 'nwat.ne.(iwat-1)',nwat,(iwat-1)
+      write(11,'(a35,i7)/') 'Total number of H2O molecules - ',nwat
+      write(11,'(/a13)') 'Atom types: '
+      write(11,1112) (i,'=',atype(i),i=1,ntype)
+      write(11,'(/a18)') 'Cell parameters: '
+      write(11,1111) 'a=',acell,'b=',bcell,'c=',ccell
+      write(11,1111) 'alpha=',alpha,'beta=',beta,'gamma=',gamma
+      write(11,1113) 'Vol=',vol
+ 1111 format(3(3x,a6,f10.6))
+ 1113 format(3x,a6,f13.6/)
+ 1112 format(6(3x,i3,a1,a5))
+
+c***********************************************
+c   physical constants and conversion factors
+      pi=4*atan(1.)
+      raddeg=180./pi
+      rg=1.98719e-3
+      r3=3.e3*rg
+      calkj=4.184
+      an=0.60223
+      barcal=an/calkj*1.e-4
+      ted=ccell
+c      yfn=1.0/dfloat(natom)
+c      yfan=an*yfn
+      yted=1./ted
+      dipwat=0.41*1.60217733*10./3.33564
+c**********************************************
+      yrc=1000./ccell
+      yrc1=100./ccell
+      yra=50./acell
+      yrb=50./bcell
+      ywz=100./(watmaz-watmiz)
+      yang=60./180.
+c------ i=1,50 corresponds to 50 possible atom types
+      do 202 i=1,50
+         icount(i)=0
+c            write(*,*)(mapcom(k),colname(k),amapmin(k),
+c     *        amapmax(k),mapid(k),k=1,nmaps)
+         do 201 j=1,1000
+            g(i,j)=0.
+            if(i.eq.1) then 
+               ndip(j)=0
+               dipx(j)=0.
+               dipy(j)=0.
+               dipz(j)=0.
+               dip (j)=0.
+               dipa(j)=0.
+               dipc(j)=0.
+            endif
+  201    continue
+  202 continue
+
+      do 205 k=1,40
+       do 204 i=1,50
+         do 203 j=1,50
+            smap(k,i,j)=0.
+  203    continue
+  204  continue
+  205 continue
+
+      do 302 i=1,50000
+         x(i)=0.
+         y(i)=0.
+         z(i)=0.
+  302 continue
+
+      do 305 k=1,60
+       do 304 i=1,100
+          angdis(k,i)=0.
+  304  continue
+  305 continue
+
+c***************************************************************************
+      iframe=0
+      jframe=0
+
+      open(9,file=inhist,status='old',form='formatted',err=999)
+c      open(9,file=inhist,status='old',form='unformatted',err=999)
+
+****************************************************************************
+ 9999 continue
+****************************************************************************        
+         iatom=0
+         itycon=0
+c----Sets counter to zero
+
+
+c---------------------------------TESTING.F 
+         read(9,*,end=999)
+         read(9,*,end=999) CurrentTime
+         read(9,*,end=999)
+         read(9,*,end=999) natom
+         read(9,*,end=999)
+         read(9,*,end=999)
+         read(9,*,end=999)
+         read(9,*,end=999)
+         read(9,*,end=999)
+
+ 400     format(i6,i3,3f9.5)
+ 410     format(1x,i5,1x,i2,3f9.5)
+         
+
+      
+         do 440 j=1,natom
+c----Comment this for a z mineral
+c 420        read(9,*,end=999) iatom,itype(iatom),z(iatom),x(iatom),
+c     *      y(iatom)
+
+c---- Uncomment this for a z mineral
+ 420        read(9,*,end=999) iatom,itype(iatom),x(iatom),y(iatom),
+     *      z(iatom)          
+
+c              write(11,400)iatom, itype(iatom), x(iatom),y(iatom),
+c     *      z(iatom)
+
+c---- itype(iatom) = current atom being read
+c---- atype(i) = list of unique atom types
+
+           do 430 i=1,itycon
+              if (itype(iatom).eq.atype(i)) goto 440
+ 430        continue 
+
+c----    increases itycon by one
+           itycon=itycon+1
+c----   icount(itycon)=0 prevents summation over all frames 
+           icount(itycon)=0
+           atype(itycon)=itype(iatom)
+           ntype=itycon
+          
+ 440    continue
+          
+c---------------------------------TESTING.F
+
+     
+         jframe=jframe+1
+         if(jframe.lt.iframe1) goto 9999
+         iframe=iframe+1
+         if(mod(iframe,100).eq.0) write(*,*) iframe, jframe
+
+         do 9997 i=1,natom
+
+            
+c----       Added to change LAMMPS fractional coords to Cart.      
+            xx=x(i) * acell
+            yy=y(i) * bcell
+            zz=(z(i)+zshift) * ccell
+c----       This section rescales atoms into the box
+
+            sx=acell*dnint(xx/acell-0.5)
+            xx=xx-sx
+            sy=bcell*dnint(yy/bcell-0.5) 
+            yy=yy-sy
+            sz=ccell*dnint(zz/ccell-0.5) 
+            zz=zz-sz
+
+            j=int(zz*yrc)+1
+            g(itype(i),j)=g(itype(i),j)+1.
+            icount(itype(i))=icount(itype(i))+1
+
+***************************************************************
+***     This part is now made universal
+***vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
+            ix=int(xx*yra)+1 
+            iy=int(yy*yrb)+1 
+            do 777 imap=1,nmaps
+              if(itype(i).eq.mapid(imap)) then
+                if((zz.ge.amapmin(imap)).and.(zz.le.amapmax(imap))) then
+                   smap(imap,ix,iy)=smap(imap,ix,iy)+1.
+
+            
+
+c---------binning occurs here with smap count of atoms at given height
+                endif
+              endif 
+  777        continue
+
+             if(itype(i).eq.otype) then
+
+                xo=x(i)
+                yo=y(i)
+                zo=z(i)+zshift
+                xh1=x(i+1)
+                xh2=x(i+2)
+                yh1=y(i+1)
+                yh2=y(i+2)
+                zh1=z(i+1)+zshift
+                zh2=z(i+2)+zshift
+
+c                sx=acell*dnint(xo/acell-0.5)
+c                xo=xo-sx
+c                xh1=xh1-sx
+c                xh2=xh2-sx
+c                sy=bcell*dnint(yo/bcell-0.5) 
+c                yo=xo-sy
+c                yh1=yh1-sy
+c                yh2=yh2-sy
+c                sz=ccell*dnint(zo/ccell-0.5) 
+c                zo=zo-sz
+c                zh1=zh1-sz
+c                zh2=zh2-sz
+
+                j=int(zz*yrc)+1
+                dipxj=dipwat*(xh1+xh2-2*xo)
+                dipyj=dipwat*(yh1+yh2-2*yo)
+                dipzj=dipwat*(zh1+zh2-2*zo)
+                dipxyj=sqrt(dipxj**2+dipyj**2)
+                dipj=sqrt(dipxyj**2+dipzj**2)
+                if(abs(dipj).gt.3.5) write(*,*) 'dip',j,dipj
+                if(dipj.ne.0.) then
+                   dipcj=dipxyj/dipj
+
+c                   if(dipcj.ge.1.) then 
+c                      write(*,*) ' dipcj ',dipcj
+c                      dipcj=0.999999
+c                   elseif(dipcj.le.-1.) then 
+c                      write(*,*) ' dipcj ',dipcj
+c                      dipcj=-0.999999
+c                   endif
+
+                   adipzj=abs(dipzj)
+                   if(adipzj.le.0.000001) then
+                      write(*,*) j,' dipzj ',dipzj
+                      dipaj=0.
+                   else
+                      dipaj=acos(dipcj)*dipzj/adipzj
+c                      dipaj=acosd(dipcj)*dipzj/adipzj
+
+c                      if(abs(dipaj).ge.89.) then
+c                         write(*,*) ' vertical dip mom:', dipaj
+c                         write(*,*) xo,yo,zo
+c                         write(*,*) xh1,yh1,zh1
+c                         write(*,*) xh2,yh2,zh2
+c                      endif
+                   endif
+                endif
+
+                dipx(j)=dipx(j)+dipxj
+                dipy(j)=dipy(j)+dipyj
+                dipz(j)=dipz(j)+dipzj
+                dip (j)=dip (j)+dipj
+                dipc(j)=dipc(j)+dipcj
+                dipa(j)=dipa(j)+dipaj
+                ndip(j)=ndip(j)+1
+
+                jj=int(zz*yrc1)+1
+                kk=int((dipaj+90.)*yang)+1
+                angdis(kk,jj)=angdis(kk,jj)+1.
+
+             endif 
+
+***^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+***     This part is now made universal
+***************************************************************
+
+ 9997    continue
+
+c      endif
+      if(iframe.ge.iframe2) goto 999
+      go to 9999
+
+ 999  continue
+      close(9)
+
+  667 format(3x,' After analysis of ',i6,' configurations: ')
+
+      write(11,667) iframe
+      write(12,667) iframe
+      write(13,667) iframe
+
+       fact=vol*yrc/(acell*bcell)
+      write(11,*) 'Normalization factor:',fact
+
+      write(11,800) (i,i=1,ntype)
+
+      write(11,'(70x,20i10)') (icount(i),i=1,ntype)
+
+ 800  format('       r  ',
+     *   '   dipX   ','   dipY   ','   dipZ   ',
+     *   '   |dip|  ','   cos_dip','   ang_dip',
+     *    27i10)
+ 
+      
+
+      do 206 i=1,1000
+         fi=dfloat(i)
+         rs1=(fi-0.5)/yrc
+         if(ndip(i).ne.0) then
+            dipx(i)=dipx(i)/ndip(i)
+            dipy(i)=dipy(i)/ndip(i)
+            dipz(i)=dipz(i)/ndip(i)
+            dip (i)=dip (i)/ndip(i)
+            dipc(i)=dipc(i)/ndip(i)
+            dipa(i)=dipa(i)/ndip(i)
+         endif
+c         write(11,444) rs1,(g(j,i)*fact/icount(j),j=1,ntype),
+         write(11,444) rs1,dipx(i),dipy(i),dipz(i),
+     *                dip(i),dipc(i),dipa(i),
+     *                (g(j,i)*fact/iframe/1000.,j=1,ntype)     
+  206 continue
+  444 format(3x, f7.3,26f10.5)
+
+      close(11)
+
+      do 1206 ii=1,nmaps
+         amamap(ii)=0.
+ 1206 continue 
+
+      do 1205 k=1,nmaps
+       do 1204 i=1,50
+         do 1203 j=1,50
+            if (amamap(k).lt.smap(k,i,j)) amamap(k)=smap(k,i,j)
+ 1203    continue
+ 1204  continue
+ 1205 continue
+
+c        write(12,446) acell,bcell,(amamap(i),i=1,nmaps)
+
+      write(12,336) (mapcom(i),mapid(i),colname(i),i=1,nmaps)
+      write(12,335) (colname(ii),ii=1,nmaps)
+
+      do 209 j=1,50
+       fj=float(j)
+       ra=(fj-0.5)/yra
+       do 210 k=1,50
+          fk=float(k)
+          rb=(fk-0.5)/yrb
+          do 211 i=1,nmaps
+            if(amamap(i).ne.0.) then
+               psmap(i)=smap(i,j,k)/amamap(i)
+            else
+               psmap(i)=0.
+            endif
+  211     continue
+
+          write(12,446) ra,rb,(psmap(i),i=1,nmaps)
+
+ 210     continue
+ 209  continue
+
+  446 format(42f8.3)
+  335 format(//'   ra      rb      ',40a8)
+  336 format(1x,a40,':   at.type - ',i5,';   col.title - ',a8)
+         
+         write(12,*) (mapcom(i),i=1,nmaps)
+         write(12,'(a40)')(mapcom(i),i=1,nmaps)
+
+      close(12)
+
+      write(13,*) '  angle ','   z    ',' angdis '
+      do 309 j=1,60
+       fj=float(j)
+       ang=(fj-0.5)/yang-90.
+       do 310 k=1,100
+          fk=float(k)
+          z1=(fk-0.5)/yrc1
+
+          write(13,446) ang,z1,angdis(j,k)/iframe
+
+ 310     continue
+ 309  continue
+
+
+      close(13)
+
+      stop
+      end

tools/micelle2d.f

@@ -0,0 +1,233 @@
+c Create LAMMPS 2003 input file for 2d LJ simulation of micelles
+c
+c Syntax: micelle2d < def.micelle2d > data.file
+c
+c def file contains size of system and number to turn into surfactants
+c attaches a random surfactant tail(s) to random head
+c if nonflag is set, will attach 2nd-neighbor bonds in surfactant
+c solvent atoms = type 1
+c micelle heads = type 2
+c micelle tails = type 3,4,5,etc.
+
+      program micelle2d
+      parameter (maxatom=100000,maxbond=10000)
+      real*4 x(2,maxatom)
+      integer type(maxatom),molecule(maxatom)
+      integer bondatom(2,maxbond),bondtype(maxbond)
+      common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
+     $     zboundlo,zboundhi
+ 999  format (3i7,3f8.3)
+ 998  format (4i7)
+
+      read (5,*)
+      read (5,*)
+      read (5,*) rhostar
+      read (5,*) iseed
+      read (5,*) nx,ny
+      read (5,*) nsurf
+      read (5,*) r0
+      read (5,*) ntails
+      read (5,*) nonflag
+      
+      natoms = nx*ny
+      if (natoms+nsurf*ntails.gt.maxatom) then
+        write (6,*) 'Too many atoms - boost maxatom'
+        call exit(0)
+      endif
+
+      nbonds = nsurf*ntails
+      if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
+      if (nbonds.gt.maxbond) then
+        write (6,*) 'Too many surfactants - boost maxbond'
+        call exit(0)
+      endif
+
+c box size
+
+      rlattice = (1.0/rhostar) ** 0.5
+
+      xboundlo = 0.0
+      xboundhi = nx*rlattice
+      yboundlo = 0.0
+      yboundhi = ny*rlattice
+      zboundlo = -0.1
+      zboundhi = 0.1
+      
+      sigma = 1.0
+
+      xprd = xboundhi - xboundlo
+      yprd = yboundhi - yboundlo
+      zprd = zboundhi - zboundlo
+
+c initial square lattice of solvents
+
+      m = 0
+      do j = 1,ny
+        do i = 1,nx
+          m = m + 1
+          x(1,m) = xboundlo + (i-1)*rlattice
+          x(2,m) = yboundlo + (j-1)*rlattice
+          molecule(m) = 0
+          type(m) = 1
+        enddo
+      enddo
+
+c turn some into surfactants with molecule ID
+c  head changes to type 2
+c  create ntails for each head of types 3,4,...
+c  each tail is at distance r0 away in straight line with random orientation
+
+      do i = 1,nsurf
+
+ 10     m = random(iseed)*natoms + 1
+        if (m.gt.natoms) m = natoms
+        if (molecule(m) .ne. 0) goto 10
+
+        molecule(m) = i
+        type(m) = 2
+
+        angle = random(iseed)*2.0*3.1415926
+        do j = 1,ntails
+          k = (i-1)*ntails + j 
+          x(1,natoms+k) = x(1,m) + cos(angle)*j*r0*sigma
+          x(2,natoms+k) = x(2,m) + sin(angle)*j*r0*sigma
+          molecule(natoms+k) = i
+          type(natoms+k) = 2+j
+          call pbc(x(1,natoms+k),x(2,natoms+k))
+          if (j.eq.1) bondatom(1,k) = m
+          if (j.ne.1) bondatom(1,k) = natoms+k-1
+          bondatom(2,k) = natoms+k
+          bondtype(k) = 1
+        enddo
+
+      enddo
+
+c if nonflag is set, add (ntails-1) 2nd nearest neighbor bonds to end
+c   of bond list
+c k = location in bondatom list where nearest neighbor bonds for
+c     this surfactant are stored
+
+      if (nonflag.eq.1) then
+
+        nbonds = nsurf*ntails
+        do i = 1,nsurf
+          do j = 1,ntails-1
+            k = (i-1)*ntails + j
+            nbonds = nbonds + 1
+            bondatom(1,nbonds) = bondatom(1,k)
+            bondatom(2,nbonds) = bondatom(2,k+1)
+            bondtype(nbonds) = 2
+          enddo
+        enddo
+
+      endif
+
+c write LAMMPS data file
+
+      natoms = natoms + nsurf*ntails
+      nbonds = nsurf*ntails
+      if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
+      ntypes = 2 + ntails
+      nbondtypes = 1
+      if (nonflag.eq.1) nbondtypes = 2
+
+      if (nsurf.eq.0) then
+        ntypes = 1
+        nbondtypes = 0
+      endif
+
+      write (6,*) 'LAMMPS 2d micelle data file'
+      write (6,*)
+
+      write (6,*) natoms,' atoms'
+      write (6,*) nbonds,' bonds'
+      write (6,*) 0,' angles'
+      write (6,*) 0,' dihedrals'
+      write (6,*) 0,' impropers'
+      write (6,*)
+
+      write (6,*) ntypes,' atom types'
+      write (6,*) nbondtypes,' bond types'
+      write (6,*) 0,' angle types'
+      write (6,*) 0,' dihedral types'
+      write (6,*) 0,' improper types'
+      write (6,*)
+
+      write (6,*) xboundlo,xboundhi,' xlo xhi'
+      write (6,*) yboundlo,yboundhi,' ylo yhi'
+      write (6,*) zboundlo,zboundhi,' zlo zhi'
+
+      write (6,*)
+      write (6,*) 'Masses'
+      write (6,*)
+
+      do i = 1,ntypes
+        write (6,*) i,1.0
+      enddo
+
+      write (6,*)
+      write (6,*) 'Atoms'
+      write (6,*)
+
+      do i = 1,natoms
+        write (6,999) i,molecule(i),type(i),x(1,i),x(2,i),0.0
+      enddo
+
+      if (nsurf.gt.0) then
+
+        write (6,*)
+        write (6,*) 'Bonds'
+        write (6,*)
+
+        do i = 1,nbonds
+          write (6,998) i,bondtype(i),bondatom(1,i),bondatom(2,i)
+        enddo
+      
+      endif
+
+c write Xmovie bond geometry file
+
+      open(1,file='bond.micelle')
+
+      write (1,*) 'ITEM: BONDS'
+      do i = 1,nbonds
+        write (1,*) bondtype(i),bondatom(1,i),bondatom(2,i)
+      enddo
+
+      close(1)
+
+      end
+
+
+c ************
+c Subroutines
+c ************
+
+c periodic boundary conditions - map atom back into periodic box
+
+      subroutine pbc(x,y)
+      common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
+     $     zboundlo,zboundhi
+
+      if (x.lt.xboundlo) x = x + xprd
+      if (x.ge.xboundhi) x = x - xprd
+      if (y.lt.yboundlo) y = y + yprd
+      if (y.ge.yboundhi) y = y - yprd
+
+      return
+      end
+
+
+c RNG - compute in double precision, return single
+      
+      real*4 function random(iseed)
+      real*8 aa,mm,sseed
+      parameter (aa=16807.0D0,mm=2147483647.0D0)
+      
+      sseed = iseed
+      sseed = mod(aa*sseed,mm)
+      random = sseed/mm
+      iseed = sseed
+
+      return
+      end

tools/msi2lmp/README

@@ -0,0 +1,132 @@
+
+ msi2lmp V3.6 4/10/2005
+
+ This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
+ program to produce a LAMMPS data file.
+
+ 1. Building msi2lmp3
+
+    Use the Makefile in the src directory. It is
+    currently set up for gcc. One will have to modify
+    it to use a different compiler.
+
+ 2. Testing the program
+
+    There are three pairs (.car and .mdf) files in the
+    test directory: crambin, nylon and phen3_cff97. The
+    atom types in crambin and nylon are cvff (Class I) atom
+    types and those in phen3_cff97 are cff9x (Class II) atom types.
+    Two forcefield files, cvff.frc and cff91.frc, are needed
+    generate lammps data files for these three test files. To
+    run it you would:
+
+   % setenv BIOSYM_LIBRARY ../biosym_frc_files
+   % ../src/msi2lmp.exe nylon -class I -frc cvff > data.nylon
+   % ../src/msi2lmp.exe crambin -class I -frc cvff > data.crambin
+   % ../src/msi2lmp.exe phen3_cff97 -class II -frc cff91 > data.phen3_cff97
+
+   Three files should be generated: data.nylon, data.crambin
+   and data.phen3_cff97. These can be compared against 
+   data.x in the directory correct. If there are differences, 
+   first recompile the program with no optimization and try again.
+   If there are still differences, send email to jec@mayo.edu
+
+   Note: you will see many "Unable to find..." parameters messages
+         in the phen3_cff97 test case. Most of those parameters 
+         exist in cff95.frc, but not in cff91.frc
+
+ 3. To run the program
+
+   The program is started by supplying information at the command prompt
+   according to the usage described below.  
+
+   USAGE: msi2lmp.exe ROOTNAME {-2001} {-print #} {-class #} {-frc FRC_FILE} 
+
+   -- msi2lmp.exe is the name of the executable
+   -- ROOTNAME is the base name of the .car and .mdf files
+   -- -2001
+         Output lammps files for LAMMPS version 2001 (F90 version)
+         The default is for LAMMPS 2005 (C++ version) 
+   -- -print 
+	 # is the print level  0 - silent except for error messages
+	                       1 - minimal (default)
+                               2 - verbose (usual for developing and
+                                   checking new data files for consistency)
+   -- -class 
+         # is the class of forcefield to use (I  = Class I e.g., CVFF)
+		  			     (II = Class II e.g., CFFx )
+      default is -class I
+
+   -- -frc   - specifies name of the forcefield file (e.g., cff91)
+ 
+     If the name includes a hard wired directory (i.e., if the name
+     starts with . or /), then the name is used alone. Otherwise,
+     the program looks for the forcefield file in $BIOSYM_LIBRARY.
+     If $BIOSYM_LIBRARY is not set, then the current directory is 
+     used.
+
+     If the file name does not include a dot after the first
+     character, then .frc is appended to the name.
+
+     For example,  -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
+                              or .)
+
+                   -frc cff/cff91 (assumes cff91.frc is in 
+                                   $BIOSYM_LIBRARY/cff or ./cff)
+
+                   -frc /usr/local/biosym/forcefields/cff95 (absolute
+                                                             location)
+
+     By default, the program uses $BIOSYM_LIBRARY/cvff.frc
+
+  -- the LAMMPS data file is written to ROOTNAME.lammps{01/05}
+     commentary is written to standard error.
+
+
+****************************************************************
+*
+* Msi2lmp3
+*
+* This is the third version of a program that generates a LAMMPS
+* data file based on the information in MSI .car (atom
+* coordinates), .mdf (molecular topology) and .frc (forcefield) 
+* files. The .car and .mdf files are specific to a molecular
+* system while the .frc file is specific to a forcefield version.
+* The only coherency needed between .frc and .car/.mdf files are
+* the atom types. 
+*
+* The first version was written by Steve Lustig at Dupont, but
+* required using Discover to derive internal coordinates and
+* forcefield parameters
+*
+* The second version was written by Michael Peachey while an
+* intern in the Cray Chemistry Applications Group managed
+* by John Carpenter. This version derived internal coordinates
+* from the mdf file and looked up parameters in the frc file
+* thus eliminating the need for Discover.
+*
+* The third version was written by John Carpenter to optimize
+* the performance of the program for large molecular systems
+* (the original  code for deriving atom numbers was quadratic in time)
+* and to make the program fully dynamic. The second version used
+* fixed dimension arrays for the internal coordinates.
+*
+* The current maintainer is only reluctantly doing so because John Mayo no longer
+* needs this code.
+*
+* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
+* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
+* for number_of_dihedrals, etc. could be unpredictable in these systems.
+*
+* V3.3 was generated in response to a strange error reading a MDF file generated by
+* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c 
+* seems to have fixed the problem.
+*
+* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
+* written by Accelys' Materials Studio GUI.
+*
+* V3.6 outputs to LAMMPS 2005 (C++ version).
+*
+* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
+* 
+* April 2005

tools/msi2lmp/biosym_frc_files/README

@@ -0,0 +1,5 @@
+
+Copy cvff.frc and cff9*.frc or any other
+.frc files you have licensed to this 
+directory for use with msi2lmp. 
+

tools/msi2lmp/biosym_frc_files/pcff.rlb

@@ -0,0 +1,2 @@
+VERSION
+elib

tools/msi2lmp/src/CheckLists.c

@@ -0,0 +1,41 @@
+#include "Msi2LMP2.h"
+
+void CheckLists() {
+  int i,j,k,ic_type;
+
+  for (i=0; i < total_no_bonds; i++) {
+    if ((atoms[bonds[i].members[0]].type != bondtypes[bonds[i].type].types[0])
+	|| (atoms[bonds[i].members[1]].type != bondtypes[bonds[i].type].types[1])) {
+      fprintf(stderr,"Warning atom types in bond %d are inconsistent with bond type %d\n",i,bonds[i].type);
+    }
+  }
+
+  for (i=0; i < total_no_angles;i++) {
+    if (   (atoms[angles[i].members[0]].type != angletypes[angles[i].type].types[0])
+	|| (atoms[angles[i].members[1]].type != angletypes[angles[i].type].types[1])
+	|| (atoms[angles[i].members[2]].type != angletypes[angles[i].type].types[2]))
+      {
+	fprintf(stderr,"Warning atom types in angle %d are inconsistent with angle type %d\n", i,angles[i].type);
+      }
+  }
+
+  for (i=0; i < total_no_dihedrals; i++) {
+    if (   (atoms[dihedrals[i].members[0]].type != dihedraltypes[dihedrals[i].type].types[0])
+	|| (atoms[dihedrals[i].members[1]].type != dihedraltypes[dihedrals[i].type].types[1])
+	|| (atoms[dihedrals[i].members[2]].type != dihedraltypes[dihedrals[i].type].types[2])
+	|| (atoms[dihedrals[i].members[3]].type != dihedraltypes[dihedrals[i].type].types[3])) {
+      fprintf(stderr,"Warning atom types in dihedral %d are inconsistent with dihedral type %d\n",i,dihedrals[i].type);
+    }
+  }
+
+  for (i=0; i < total_no_oops; i++) {
+
+    if (   (atoms[oops[i].members[0]].type != ooptypes[oops[i].type].types[0])
+	|| (atoms[oops[i].members[1]].type != ooptypes[oops[i].type].types[1])
+	|| (atoms[oops[i].members[2]].type != ooptypes[oops[i].type].types[2])
+	|| (atoms[oops[i].members[3]].type != ooptypes[oops[i].type].types[3]))
+      {
+	fprintf(stderr,"Warning atom types in oop %d are inconsistent with oop type %d\n",i,oops[i].type);
+      }
+  }
+}

tools/msi2lmp/src/Forcefield.h

@@ -0,0 +1,47 @@
+/******************************
+*
+*   This is the header file for the routine that reads the forcefield file
+*   into memory in order to speed up searching.
+*
+*   It defines the data structures used to store the force field in memory
+*/
+
+#include <stdio.h>
+#include <string.h>
+#include <stddef.h>
+#include <stdlib.h>
+
+
+#ifdef	FF_MAIN
+#define _EX
+#else
+#define _EX	extern
+#endif
+
+#define MAX_NO_MEMS 5
+#define MAX_NO_PARAMS 8
+#define MAX_LINE 200
+
+struct FrcFieldData
+{
+  float 	ver;		/* Version number of forcefield entry */
+  int		ref;		/* Reference within forcefield */
+  char	        ff_types[MAX_NO_MEMS][5];
+  double        ff_param[MAX_NO_PARAMS];
+};
+
+struct FrcFieldItem
+{
+  char		keyword[25];
+  int		number_of_members;	/* number of members of item */
+  int		number_of_parameters;	/* number of parameters of item */
+  int 		entries;		/* number of entries in item list */
+  struct FrcFieldData *data;		/* contains all eqiuv and param data */
+};
+
+_EX	struct	FrcFieldItem ff_atomtypes, equivalence, \
+		ff_vdw,ff_bond, ff_ang, ff_tor, ff_oop, \
+		ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, \
+                ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13;
+
+#undef _EX

tools/msi2lmp/src/InitializeItems.c

@@ -0,0 +1,125 @@
+/*
+*   This function fills in the keyword field, the number of members for each
+*   item and the number of parameters for each item
+*
+*/
+
+#include "Forcefield.h"
+#include "Msi2LMP2.h"
+
+void InitializeItems(void)
+{
+   /* ATOM TYPES */
+   strcpy(ff_atomtypes.keyword,"#atom_types");
+   ff_atomtypes.number_of_members = 1;
+   ff_atomtypes.number_of_parameters = 1;
+
+   /* EQUIVALENCE */
+
+   strcpy(equivalence.keyword, "#equivalence");
+   equivalence.number_of_members = 6;
+   equivalence.number_of_parameters = 0;
+
+   /* NON-BOND */
+   strcpy(ff_vdw.keyword, "#nonbond");
+   ff_vdw.number_of_members = 1;
+   ff_vdw.number_of_parameters = 2;
+
+   /* BOND */
+   ff_bond.number_of_members = 2;
+   if(forcefield == 1) {
+     strcpy(ff_bond.keyword, "#quadratic_bond");
+     ff_bond.number_of_parameters = 2;
+   }
+   else {
+     strcpy(ff_bond.keyword, "#quartic_bond");
+     ff_bond.number_of_parameters = 4;
+   }
+
+   /* ANGLE */
+
+   ff_ang.number_of_members = 3;
+   if(forcefield ==1)
+   {
+      strcpy(ff_ang.keyword, "#quadratic_angle");
+      ff_ang.number_of_parameters = 2;
+   }
+   else {
+      strcpy(ff_ang.keyword, "#quartic_angle");
+      ff_ang.number_of_parameters = 4;
+   }
+
+   /* TORSION */
+
+   ff_tor.number_of_members = 4;
+   if (forcefield == 1) {
+     strcpy(ff_tor.keyword, "#torsion_1");
+     ff_tor.number_of_parameters = 3;
+   }
+   else {
+      strcpy(ff_tor.keyword, "#torsion_3");
+      ff_tor.number_of_parameters = 6;
+   }
+
+   /* OOP */
+
+   ff_oop.number_of_members = 4;
+   if(forcefield == 1) {
+     strcpy(ff_oop.keyword, "#out_of_plane");
+     ff_oop.number_of_parameters = 3;
+   }
+   else {
+     strcpy(ff_oop.keyword,"#wilson_out_of_plane");
+     ff_oop.number_of_parameters = 2;
+   }
+
+   if (forcefield == 1) return; /* Do not try to read cross terms for Class I forcefield */
+
+   /* BOND-BOND */
+
+   strcpy(ff_bonbon.keyword, "#bond-bond");
+   ff_bonbon.number_of_members = 3;
+   ff_bonbon.number_of_parameters = 1;
+
+   /* BOND-ANGLE */
+
+   strcpy(ff_bonang.keyword, "#bond-angle");
+   ff_bonang.number_of_members = 3;
+   ff_bonang.number_of_parameters = 2;
+
+   /* ANGLE-TORSION */
+
+   strcpy(ff_angtor.keyword, "#angle-torsion_3");
+   ff_angtor.number_of_members = 4;
+   ff_angtor.number_of_parameters = 6;
+
+   /* ANGLE-ANGLE-TORSION */
+
+   strcpy(ff_angangtor.keyword,"#angle-angle-torsion_1");
+   ff_angangtor.number_of_members = 4;
+   ff_angangtor.number_of_parameters = 1;
+
+   /* END-BOND-TORSION */
+
+   strcpy(ff_endbontor.keyword, "#end_bond-torsion_3");
+   ff_endbontor.number_of_members = 4;
+   ff_endbontor.number_of_parameters = 6;
+
+   /* MID-BOND-TORSION */
+
+   strcpy(ff_midbontor.keyword,"#middle_bond-torsion_3");
+   ff_midbontor.number_of_members = 4;
+   ff_midbontor.number_of_parameters = 3;
+
+   /* ANGLE-ANGLE */
+
+   strcpy(ff_angang.keyword, "#angle-angle");
+   ff_angang.number_of_members = 4;
+   ff_angang.number_of_parameters = 1;
+
+   /* BOND-BOND-1-3 */
+
+   strcpy(ff_bonbon13.keyword, "#bond-bond_1_3");
+   ff_bonbon13.number_of_members = 4;
+   ff_bonbon13.number_of_parameters = 1;
+}

tools/msi2lmp/src/MakeLists.c

@@ -0,0 +1,783 @@
+#include "Msi2LMP2.h"
+
+int count_bonds();
+int count_angles();
+int count_dihedrals();
+int count_oops();
+int count_angle_angles();
+
+void build_bonds_list();
+void build_angles_list();
+void build_dihedrals_list();
+void build_oops_list();
+void build_angleangles_list();
+
+void build_atomtypes_list();
+void build_bondtypes_list();
+void build_angletypes_list();
+void build_dihedraltypes_list();
+void build_ooptypes_list();
+void build_angleangletypes_list();
+
+void swap_ints(int *,int *);
+void bubble_sort(int, int *, int *);
+
+/*#define PRINT_LISTS */
+
+void MakeLists()
+{
+
+  total_no_bonds = count_bonds();
+  total_no_angles = count_angles();
+  total_no_dihedrals = count_dihedrals();
+  total_no_oops = count_oops();
+  total_no_angle_angles = count_angle_angles();
+
+
+  atomtypes = (struct AtomTypeList *)calloc(MAX_ATOM_TYPES,
+					    sizeof(struct AtomTypeList));
+  if (atomtypes == NULL) {
+    fprintf(stderr,"Trouble allocating memory for atomtypes list - Exiting\n");
+    exit(1);
+  }
+
+  build_atomtypes_list();
+
+
+  if (total_no_bonds > 0) {
+    bonds = (struct BondList *)calloc(total_no_bonds,sizeof(struct BondList));
+    if (bonds == NULL) {
+      fprintf(stderr,"Trouble allocating memory for bonds list - Exiting\n");
+      exit(1);
+    }
+
+    build_bonds_list();
+
+    bondtypes = (struct BondTypeList *)calloc(MAX_BOND_TYPES,
+					    sizeof(struct BondTypeList));
+    if (bondtypes == NULL) {
+      fprintf(stderr,"Trouble allocating memory for bondtypes list - Exiting\n");
+      exit(1);
+    }
+
+    build_bondtypes_list();
+  }
+
+  if (total_no_angles > 0) {
+    angles = (struct AngleList *)calloc(total_no_angles,
+					sizeof(struct AngleList));
+    if (angles == NULL) {
+      fprintf(stderr,"Trouble allocating memory for angles list - Exiting\n");
+      exit(1);
+    }
+
+    build_angles_list();
+
+    angletypes = (struct AngleTypeList *)calloc(MAX_ANGLE_TYPES,
+					      sizeof(struct AngleTypeList));
+    if (angletypes == NULL) {
+      fprintf(stderr,"Trouble allocating memory for angletypes list - Exiting\n");
+      exit(1);
+    }
+
+    build_angletypes_list();
+  }
+
+  if (total_no_dihedrals > 0) {
+
+    dihedrals = (struct DihedralList *)calloc(total_no_dihedrals,
+					      sizeof(struct DihedralList));
+    if (dihedrals == NULL) {
+      fprintf(stderr,"Trouble allocating memory for dihedrals list - Exiting\n");
+      exit(1);
+    }
+
+    build_dihedrals_list();
+
+    dihedraltypes = (struct DihedralTypeList *)calloc(MAX_DIHEDRAL_TYPES,
+	  			  sizeof(struct DihedralTypeList));
+    if (dihedraltypes == NULL) {
+      fprintf(stderr,"Trouble allocating memory for dihedraltypes list - Exiting\n");
+      exit(1);
+    }
+
+    build_dihedraltypes_list();
+  }
+
+  if (total_no_oops > 0) {
+    oops = (struct OOPList *)calloc(total_no_oops,sizeof(struct OOPList));
+    if (oops == NULL) {
+      fprintf(stderr,"Trouble allocating memory for oops list - Exiting\n");
+      exit(1);
+    }
+    build_oops_list();
+
+    ooptypes = (struct OOPTypeList *)calloc(MAX_OOP_TYPES,
+					  sizeof(struct OOPTypeList));
+    if (ooptypes == NULL) {
+      fprintf(stderr,"Trouble allocating memory for ooptypes list - Exiting\n");
+      exit(1);
+    }
+
+    build_ooptypes_list();
+  }
+
+  if ((forcefield > 1) & (total_no_angle_angles > 0)) {
+
+    angleangles = (struct AngleAngleList *)calloc(total_no_angle_angles,
+					     sizeof(struct AngleAngleList));
+    if (angleangles == NULL) {
+      fprintf(stderr,"Trouble allocating memory for angleangles list - Exiting\n");
+      exit(1);
+    }
+    build_angleangles_list();
+
+    angleangletypes = (struct AngleAngleTypeList *)calloc(MAX_ANGLEANGLE_TYPES,
+					  sizeof(struct AngleAngleTypeList));
+    if (angleangletypes == NULL) {
+      fprintf(stderr,"Trouble allocating memory for angleangletypes list - Exiting\n");
+      exit(1);
+    }
+    build_angleangletypes_list();
+  }
+
+
+#ifdef PRINT_LISTS
+  fprintf(stderr,"Atom Types\n N Potential\n");
+  for (i=0; i < no_atom_types; i++) {
+    fprintf(stderr," %d %s\n",i,atomtypes[i].potential);
+  }
+
+  fprintf(stderr,"Atoms\n");
+  for (i=0; i < total_no_atoms; i++) {
+    fprintf(stderr,"Atom %3d %2d %-5s  %7.4f  %9.6f %9.6f %9.6f\n",
+	   i,atoms[i].type,atoms[i].potential,atoms[i].q,
+	   atoms[i].x[0],atoms[i].x[1],atoms[i].x[2]);
+  }
+
+  if (total_no_bonds > 0) {
+    fprintf(stderr,"Bond Types\n");
+    for (i=0; i < no_bond_types; i++) {
+      fprintf(stderr," %d  %d %d  %-s %-s\n",i,bondtypes[i].types[0],
+	      bondtypes[i].types[1],
+	      atomtypes[bondtypes[i].types[0]].potential,
+	      atomtypes[bondtypes[i].types[1]].potential);
+    }
+
+    fprintf(stderr,"Bonds\n N  Type  I J\n");
+    for (i=0; i < total_no_bonds; i++) {
+      fprintf(stderr," %d %d %d %d\n",i,bonds[i].type,
+	      bonds[i].members[0],
+	      bonds[i].members[1]);
+    }
+  }
+
+  if (total_no_angles > 0) {
+    fprintf(stderr,"Angle Types\n");
+    for (i=0; i < no_angle_types; i++) {
+      fprintf(stderr," %d  %d %d %d  %-s %-s %-s\n",i,angletypes[i].types[0],
+	      angletypes[i].types[1],angletypes[i].types[2],
+	      atomtypes[angletypes[i].types[0]].potential,
+	      atomtypes[angletypes[i].types[1]].potential,
+	      atomtypes[angletypes[i].types[2]].potential);
+    }
+    
+    fprintf(stderr,"Angles\n N  Type  I  J  K\n");
+    for (i=0; i < total_no_angles; i++) {
+      fprintf(stderr," %d %d %d %d %d\n",i,angles[i].type,
+	      angles[i].members[0],
+	      angles[i].members[1],
+	      angles[i].members[2]);
+    }
+  }
+
+  if (total_no_dihedrals > 0) {
+    fprintf(stderr,"Dihedral Types\n");
+    for (i=0; i < no_dihedral_types; i++) {
+      fprintf(stderr," %d  %d %d %d %d %-s %-s %-s %-s\n",i,
+	      dihedraltypes[i].types[0],
+	      dihedraltypes[i].types[1],
+	      dihedraltypes[i].types[2],
+	      dihedraltypes[i].types[3],
+	      atomtypes[dihedraltypes[i].types[0]].potential,
+	      atomtypes[dihedraltypes[i].types[1]].potential,
+	      atomtypes[dihedraltypes[i].types[2]].potential,
+	      atomtypes[dihedraltypes[i].types[3]].potential);
+    }
+
+    fprintf(stderr,"Dihedrals\n N  Type  I  J  K  L\n");
+    for (i=0; i < total_no_dihedrals; i++) {
+      fprintf(stderr," %d %d %d %d %d %d\n",i,dihedrals[i].type,
+	      dihedrals[i].members[0],
+	      dihedrals[i].members[1],
+	      dihedrals[i].members[2],
+	      dihedrals[i].members[3]);
+    }
+  }
+
+  if (total_no_oops > 0) {
+    fprintf(stderr,"Oop Types\n");
+    for (i=0; i < no_oop_types; i++) {
+      fprintf(stderr," %d  %d %d %d %d %-s %-s %-s %-s\n",i,
+	      ooptypes[i].types[0],
+	      ooptypes[i].types[1],
+	      ooptypes[i].types[2],
+	      ooptypes[i].types[3],
+	      atomtypes[ooptypes[i].types[0]].potential,
+	      atomtypes[ooptypes[i].types[1]].potential,
+	      atomtypes[ooptypes[i].types[2]].potential,
+	      atomtypes[ooptypes[i].types[3]].potential);
+    }
+
+    fprintf(stderr,"Oops\n N  Type  I  J  K  L\n");
+    for (i=0; i < total_no_oops; i++) {
+      fprintf(stderr," %d %d %d %d %d %d\n",i,oops[i].type,
+	      oops[i].members[0],
+	      oops[i].members[1],
+	      oops[i].members[2],
+	      oops[i].members[3]);
+    }
+  }
+
+  if ((forcefield > 1) & (total_no_angle_angles > 0)) {
+
+    fprintf(stderr,"Angleangle Types\n");
+    for (i=0; i < no_angleangle_types; i++) {
+      fprintf(stderr," %d  %d %d %d %d %-s %-s %-s %-s\n",i,
+	     angleangletypes[i].types[0],
+	     angleangletypes[i].types[1],
+	     angleangletypes[i].types[2],
+	     angleangletypes[i].types[3],
+	     atomtypes[angleangletypes[i].types[0]].potential,
+	     atomtypes[angleangletypes[i].types[1]].potential,
+	     atomtypes[angleangletypes[i].types[2]].potential,
+	     atomtypes[angleangletypes[i].types[3]].potential);
+    }
+    fprintf(stderr,"AngleAngles\n N  Type  I  J  K  L\n");
+    for (i=0; i < total_no_angle_angles; i++) {
+      fprintf(stderr," %d %d %d %d %d %d\n",i,angleangles[i].type,
+	     angleangles[i].members[0],
+	     angleangles[i].members[1],
+	     angleangles[i].members[2],
+	     angleangles[i].members[3]);
+    }
+  }
+#endif
+
+  if (pflag > 1) {
+    fprintf(stderr,"\n");
+    fprintf(stderr," Number of bonds, types = %7d %3d\n",
+	    total_no_bonds,no_bond_types);
+    fprintf(stderr," Number of angles, types = %7d %3d\n",
+	    total_no_angles, no_angle_types);
+    fprintf(stderr," Number of dihedrals, types = %7d %3d\n",
+	    total_no_dihedrals, no_dihedral_types);
+    fprintf(stderr," Number of out-of-planes, types = %7d %3d\n",
+	    total_no_oops, no_oop_types);
+    if (forcefield ==2)
+      fprintf(stderr," Number of Angle Angle Terms, types =   %7d %3d\n",
+	      total_no_angle_angles, no_angleangle_types);
+  }
+}
+
+int count_bonds()
+{
+  int i,j,n;
+
+  for (n=0,i=0; i < total_no_atoms; i++) {
+    for (j=0; j < atoms[i].no_connect; j++) {
+      if (i < atoms[i].conn_no[j]) n++;
+    }
+  }
+  return n;
+}
+
+void build_bonds_list()
+{
+  int i,j,n;
+
+  for (n=0,i=0; i < total_no_atoms; i++) {
+    for (j=0; j < atoms[i].no_connect; j++) {
+      if (i < atoms[i].conn_no[j]) {
+	bonds[n  ].type = 0;
+	bonds[n  ].members[0] = i;
+	bonds[n++].members[1] = atoms[i].conn_no[j];
+      }
+    }
+  }
+return;
+}
+
+int count_angles() 
+{
+  int i,j,k,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    if (atoms[j].no_connect > 1) {
+      for (i=0; i < atoms[j].no_connect-1; i++) {
+	for (k=i+1; k < atoms[j].no_connect; k++) {
+	  n++;
+	}
+      }
+    }
+  }
+  return n;
+}
+
+void build_angles_list()
+{
+  int i,j,k,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    if (atoms[j].no_connect > 1) {
+      for (i=0; i < atoms[j].no_connect-1; i++) {
+	for (k=i+1; k < atoms[j].no_connect; k++) {
+	  angles[n  ].type = 0;
+	  angles[n  ].members[0] = atoms[j].conn_no[i];
+	  angles[n  ].members[1] = j;
+	  angles[n++].members[2] = atoms[j].conn_no[k];
+	}
+      }
+    }
+  }
+return;
+}
+
+int count_dihedrals()
+{
+  int i,j,k,l,n;
+  int ii,kk,ll;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    if (atoms[j].no_connect > 1) {
+      for (kk=0; kk < atoms[j].no_connect; kk++) {
+	k = atoms[j].conn_no[kk];
+	if (atoms[k].no_connect > 1) {
+	  if (j < k) {
+	    for (ii=0; ii < atoms[j].no_connect; ii++) {
+	      i = atoms[j].conn_no[ii];
+	      if (i != k) {
+		for (ll=0; ll < atoms[k].no_connect; ll++) {
+		  l = atoms[k].conn_no[ll];
+		  if (l != j) n++;
+		}
+	      }
+	    }
+	  }
+	}
+      }
+    }
+  }
+  return n;
+}
+
+void build_dihedrals_list()
+{
+  int i,j,k,l,n;
+  int ii,kk,ll;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    if (atoms[j].no_connect > 1) {
+      for (kk=0; kk < atoms[j].no_connect; kk++) {
+	k = atoms[j].conn_no[kk];
+	if (atoms[k].no_connect > 1) {
+	  if (j < k) {
+	    for (ii=0; ii < atoms[j].no_connect; ii++) {
+	      i = atoms[j].conn_no[ii];
+	      if (i != k) {
+		for (ll=0; ll < atoms[k].no_connect; ll++) {
+		  l = atoms[k].conn_no[ll];
+		  if (l != j) {
+		    dihedrals[n  ].type = 0;
+		    dihedrals[n  ].members[0] = i;
+		    dihedrals[n  ].members[1] = j;
+		    dihedrals[n  ].members[2] = k;
+		    dihedrals[n++].members[3] = l;
+		  }
+		}
+	      }
+	    }
+	  }
+	}
+      }
+    }
+  }
+  return;
+}
+
+int
+count_oops()
+{
+  int j,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    if (atoms[j].no_connect == 3) n++;
+  }
+  return n;
+}
+
+void build_oops_list()
+{
+  int j,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+
+    if (atoms[j].no_connect == 3) {
+      oops[n  ].type = 0;
+      oops[n  ].members[0] = atoms[j].conn_no[0];
+      oops[n  ].members[1] = j;
+      oops[n  ].members[2] = atoms[j].conn_no[1];
+      oops[n++].members[3] = atoms[j].conn_no[2];
+    }
+  }
+  return;
+}
+
+int count_angle_angles()
+{
+  int num_triples[10] = {0,0,0,4,10,20,35,56,84,120};
+  int j,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    n += num_triples[atoms[j].no_connect-1];
+  }
+  return n;
+}
+
+void build_angleangles_list()
+{
+  int i,j,k,l,nc,n;
+
+  for (n=0,j=0; j < total_no_atoms; j++) {
+    nc = atoms[j].no_connect;
+    if (nc > 3) {
+      for (i=0; i < nc-2; i++) {
+	for (k=i+1; k < nc-1; k++) {
+	  for (l=k+1; l < nc; l++) {
+	    angleangles[n].type = 0;
+	    angleangles[n  ].members[0] = atoms[j].conn_no[i];
+	    angleangles[n  ].members[1] = j;
+	    angleangles[n  ].members[2] = atoms[j].conn_no[k];
+	    angleangles[n++].members[3] = atoms[j].conn_no[l];
+	  }
+	}
+      }
+    }
+  }
+  return;
+}
+
+
+void build_atomtypes_list()
+{
+  int j,k,n,match,atom_type;
+
+  strncpy(atomtypes[0].potential,atoms[0].potential,5);
+  atoms[0].type = 0;
+
+  atomtypes[0].no_connect = atoms[0].no_connect;
+
+  for (n=1,j=1; j < total_no_atoms; j++) {
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if (strncmp(atomtypes[k].potential,atoms[j].potential,5) == 0) {
+	match = 1;
+	atom_type = k;
+	if (atomtypes[k].no_connect != atoms[j].no_connect) {
+	  if (pflag > 0) fprintf(stderr," WARNING inconsistent # of connects on atom %d type %s\n",j,
+		 atomtypes[k].potential);
+	}
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+      atom_type = n;
+      atomtypes[n].no_connect = atoms[j].no_connect;
+      strncpy(atomtypes[n++].potential,atoms[j].potential,5);
+    }
+    if (n >= MAX_ATOM_TYPES) {
+      fprintf(stderr,"Too many atom types (> 100) - error\n");
+      exit(1);
+    }
+    atoms[j].type = atom_type;
+  }
+  no_atom_types = n;
+  return;
+}
+
+void build_bondtypes_list() {
+  int j,k,n,match,bond_type;
+  int typei,typej;
+
+  for (n=0,j=0; j < total_no_bonds; j++) {
+    typei = atoms[bonds[j].members[0]].type;
+    typej = atoms[bonds[j].members[1]].type;
+    if (typej < typei) {
+      swap_ints(&typei,&typej);
+      swap_ints(&bonds[j].members[0],&bonds[j].members[1]);
+    }
+
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if ((typei == bondtypes[k].types[0]) &&
+	  (typej == bondtypes[k].types[1])) {
+	match = 1;
+	bond_type = k;
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+      bond_type = n;
+      bondtypes[n  ].types[0] = typei;
+      bondtypes[n++].types[1] = typej;
+    }
+    if (n >= MAX_BOND_TYPES) {
+      fprintf(stderr,"Too many bond types (> 200) - error\n");
+      exit(1);
+    }
+
+    bonds[j].type = bond_type;
+  }
+  no_bond_types = n;
+  return;
+}
+
+void build_angletypes_list()
+{
+  int j,k,n,match,angle_type;
+  int typei,typej,typek;
+
+  for (n=0,j=0; j < total_no_angles; j++) {
+    typei = atoms[angles[j].members[0]].type;
+    typej = atoms[angles[j].members[1]].type;
+    typek = atoms[angles[j].members[2]].type;
+    if (typek < typei) {
+      swap_ints(&typei,&typek);
+      swap_ints(&angles[j].members[0],&angles[j].members[2]);
+    }
+
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if ((typei == angletypes[k].types[0]) &&
+	  (typej == angletypes[k].types[1]) &&
+	  (typek == angletypes[k].types[2])) {
+	match = 1;
+	angle_type = k;
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+      angle_type = n;
+      angletypes[n  ].types[0] = typei;
+      angletypes[n  ].types[1] = typej;
+      angletypes[n++].types[2] = typek;
+    }
+    if (n >= MAX_ANGLE_TYPES) {
+      fprintf(stderr,"Too many angle types (> 300) - error\n");
+      exit(1);
+    }
+    angles[j].type = angle_type;
+  }
+  no_angle_types = n;
+  return;
+}
+
+void build_dihedraltypes_list()
+{
+  int j,k,n,match,dihedral_type;
+  int typei,typej,typek,typel;
+
+  for (n=0,j=0; j < total_no_dihedrals; j++) {
+    typei = atoms[dihedrals[j].members[0]].type;
+    typej = atoms[dihedrals[j].members[1]].type;
+    typek = atoms[dihedrals[j].members[2]].type;
+    typel = atoms[dihedrals[j].members[3]].type;
+    if ((typek < typej) || ((typej == typek) && (typel < typei))) {
+      swap_ints(&typej,&typek);
+      swap_ints(&dihedrals[j].members[1],&dihedrals[j].members[2]);
+      swap_ints(&typei,&typel);
+      swap_ints(&dihedrals[j].members[0],&dihedrals[j].members[3]);
+    }
+
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if ((typei == dihedraltypes[k].types[0]) &&
+	  (typej == dihedraltypes[k].types[1]) &&
+	  (typek == dihedraltypes[k].types[2]) &&
+	  (typel == dihedraltypes[k].types[3])) {
+	match = 1;
+	dihedral_type = k;
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+      dihedral_type = n;
+      dihedraltypes[n  ].types[0] = typei;
+      dihedraltypes[n  ].types[1] = typej;
+      dihedraltypes[n  ].types[2] = typek;
+      dihedraltypes[n++].types[3] = typel;
+    }
+    if (n >= MAX_DIHEDRAL_TYPES) {
+      fprintf(stderr,"Too many dihedral types (> 400) - error\n");
+      exit(1);
+    }
+    dihedrals[j].type = dihedral_type;
+  }
+  no_dihedral_types = n;
+  return;
+}
+
+void build_ooptypes_list()
+{
+  int j,k,n,match,oop_type;
+  int temp_types[3],temp_pos[3];
+  int typei,typej,typek,typel;
+
+  for (n=0,j=0; j < total_no_oops; j++) {
+    typei = atoms[oops[j].members[0]].type;
+    typej = atoms[oops[j].members[1]].type;
+    typek = atoms[oops[j].members[2]].type;
+    typel = atoms[oops[j].members[3]].type;
+    temp_types[0] = typei;
+    temp_types[1] = typek;
+    temp_types[2] = typel;
+
+    bubble_sort(3,temp_types,temp_pos);
+
+    typei = temp_types[0];
+    typek = temp_types[1];
+    typel = temp_types[2];
+    temp_types[0] = oops[j].members[0];
+    temp_types[1] = oops[j].members[2];
+    temp_types[2] = oops[j].members[3];
+    oops[j].members[0] = temp_types[temp_pos[0]];
+    oops[j].members[2] = temp_types[temp_pos[1]];
+    oops[j].members[3] = temp_types[temp_pos[2]];
+
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if ((typei == ooptypes[k].types[0]) &&
+	  (typej == ooptypes[k].types[1]) &&
+	  (typek == ooptypes[k].types[2]) &&
+	  (typel == ooptypes[k].types[3])) {
+	match = 1;
+	oop_type = k;
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+
+      oop_type = n;
+      ooptypes[n  ].types[0] = typei;
+      ooptypes[n  ].types[1] = typej;
+      ooptypes[n  ].types[2] = typek;
+      ooptypes[n++].types[3] = typel;
+    }
+    if (n >= MAX_OOP_TYPES) {
+      fprintf(stderr,"Too many oop types (> 400) - error\n");
+      exit(1);
+    }
+    oops[j].type = oop_type;
+  }
+  no_oop_types = n;
+  return;
+}
+
+void build_angleangletypes_list()
+{
+  int j,k,n,match,angleangle_type;
+  int temp_types[3],temp_pos[3];
+  int typei,typej,typek,typel;
+
+  for (n=0,j=0; j < total_no_angle_angles; j++) {
+
+    typei = atoms[angleangles[j].members[0]].type;
+    typej = atoms[angleangles[j].members[1]].type;
+    typek = atoms[angleangles[j].members[2]].type;
+    typel = atoms[angleangles[j].members[3]].type;
+
+    temp_types[0] = typei;
+    temp_types[1] = typek;
+    temp_types[2] = typel;
+
+    bubble_sort(3,temp_types,temp_pos);
+
+    typei = temp_types[0];
+    typek = temp_types[1];
+    typel = temp_types[2];
+
+    temp_types[0] = angleangles[j].members[0];
+    temp_types[1] = angleangles[j].members[2];
+    temp_types[2] = angleangles[j].members[3];
+
+    angleangles[j].members[0] = temp_types[temp_pos[0]];
+    angleangles[j].members[2] = temp_types[temp_pos[1]];
+    angleangles[j].members[3] = temp_types[temp_pos[2]];
+
+    match = 0;
+    k = 0;
+    while (!match && (k < n)) {
+      if ((typei == angleangletypes[k].types[0]) &&
+	  (typej == angleangletypes[k].types[1]) &&
+	  (typek == angleangletypes[k].types[2]) &&
+	  (typel == angleangletypes[k].types[3])) {
+	match = 1;
+	angleangle_type = k;
+      }
+      else
+	k++;
+    }
+    if (match == 0) {
+      angleangle_type = n;
+      angleangletypes[n  ].types[0] = typei;
+      angleangletypes[n  ].types[1] = typej;
+      angleangletypes[n  ].types[2] = typek;
+      angleangletypes[n++].types[3] = typel;
+    }
+
+    if (n >= MAX_ANGLEANGLE_TYPES) {
+      fprintf(stderr,"Too many angleangle types (> 400) - error\n");
+      exit(1);
+    }
+    angleangles[j].type = angleangle_type;
+  }
+  no_angleangle_types = n;
+  return;
+}
+
+void swap_ints(int *i, int *j)
+{
+  int temp;
+
+  temp = *i;
+  *i = *j;
+  *j = temp;
+
+  return;
+}
+
+void bubble_sort(int n, int *val, int *pos)
+{
+  int i,j;
+
+  for (i=0; i < n; i++) pos[i] = i;
+  for (i=0; i < n-1; i++) {
+    for (j=1; j < n; j++) {
+      if (val[j] < val[i]) {
+	swap_ints(&val[i],&val[j]);
+	swap_ints(&pos[i],&pos[j]);
+      }
+    }
+  }
+}
+

tools/msi2lmp/src/Makefile

@@ -0,0 +1,37 @@
+
+TARGET	 = msi2lmp.exe
+
+SRCS     = msi2lmp.c \
+           ReadCarFile.c \
+           ReadMdfFile.c \
+	   MakeLists.c \
+           ReadFrcFile.c \
+           InitializeItems.c \
+	   SearchAndFill.c \
+           GetParameters.c \
+	   CheckLists.c \
+           WriteDataFile05.c \
+           WriteDataFile01.c
+
+OBJS     = $(SRCS:.c=.o)
+
+HEADERS  = Msi2LMP2.h Forcefield.h
+
+CC       = gcc
+CFLAGS   = -O2
+FRCFILE  = cvff.frc
+FRCFILE2 = cff91.frc
+README   = README
+MKFILE   = Makefile
+
+$(TARGET) : $(OBJS)
+	$(CC) $(CFLAGS) -o $(TARGET) $(OBJS) -lm
+
+$(OBJS) : $(HEADERS)
+
+.c.o:
+	$(CC) $(CFLAGS) -c $<
+clean:
+	rm -f $(OBJS) $(TARGET)
+
+

tools/msi2lmp/src/Msi2LMP2.h

@@ -0,0 +1,209 @@
+/********************************
+*
+* Header file for Msi2LMP2 conversion program.
+*
+* Msi2lmp3
+*
+* This is the header file for the third version of a program
+* that generates a LAMMPS data file based on the information
+* in an MSI car file (atom coordinates) and mdf file (molecular
+* topology). A key part of the program looks up forcefield parameters
+* from an MSI frc file.
+*
+* The first version was written by Steve Lustig at Dupont, but
+* required using Discover to derive internal coordinates and
+* forcefield parameters
+*
+* The second version was written by Michael Peachey while an
+* intern in the Cray Chemistry Applications Group managed
+* by John Carpenter. This version derived internal coordinates
+* from the mdf file and looked up parameters in the frc file
+* thus eliminating the need for Discover.
+*
+* The third version was written by John Carpenter to optimize
+* the performance of the program for large molecular systems
+* (the original code for derving atom numbers was quadratic in time)
+* and to make the program fully dynamic. The second version used
+* fixed dimension arrays for the internal coordinates.
+*
+* John Carpenter can be contacted by sending email to
+* jec374@earthlink.net
+*
+* November 2000
+*
+*/
+
+# include <string.h>
+# include <stddef.h>
+# include <stdio.h>
+# include <stdlib.h>
+# include <math.h>
+
+#ifdef   MAIN
+#define  _EX
+#define  _ARG(arg)    = (arg)
+#else
+#define  _EX extern
+#define  _ARG(arg)
+#endif
+
+#define MAX_ATOM_TYPES 100
+#define MAX_BOND_TYPES 200
+#define MAX_ANGLE_TYPES 300
+#define MAX_DIHEDRAL_TYPES 400
+#define MAX_OOP_TYPES 400
+#define MAX_ANGLEANGLE_TYPES 400
+#define MAX_TYPES 12000
+#define MAX_MEMBERS  5
+#define MAX_LINE_LENGTH   200
+#define MAX_PARAMS        8
+#define PI_180  0.01745329252
+#define MAX_CONNECTIONS 6
+#define MAX_STRING 50
+
+struct ResidueList {
+  int start;
+  int end;
+  char name[16];
+};
+
+struct MoleculeList {
+  int start;
+  int end;
+  int no_residues;
+  struct ResidueList *residue;
+};
+
+/* Internal coodinate Lists */
+
+struct BondList {
+  int type;
+  int members[2];
+};
+
+struct AngleList {
+  int type;
+  int members[3];
+};
+
+struct DihedralList {
+  int type;
+  int members[4];
+};
+
+struct OOPList {
+  int type;
+  int members[4];
+};
+
+struct AngleAngleList {
+  int type;
+  int members[4];
+};
+
+/* Internal coodinate Types Lists */
+
+
+struct AtomTypeList
+{
+  char potential[5];
+  float mass;
+  double params[2];
+  int no_connect;
+};
+
+struct BondTypeList {
+  int types[2];
+  double params[4];
+};
+
+struct AngleTypeList {
+  int types[3];
+  double params[4];
+  double bondangle_cross_term[4];
+  double bondbond_cross_term[3];
+};
+
+struct DihedralTypeList {
+  int types[4];
+  double params[6];
+  double endbonddihedral_cross_term[8];
+  double midbonddihedral_cross_term[4];
+  double angledihedral_cross_term[8];
+  double angleangledihedral_cross_term[3];
+  double bond13_cross_term[3];
+};
+
+struct OOPTypeList {
+  int types[4];
+  double params[3];
+  double angleangle_params[6];
+};
+
+struct AngleAngleTypeList {
+  int types[4];
+  double params[6];
+};
+
+/* ---------------------------------------------- */
+
+struct Atom {
+  int   molecule;      /* molecule id */
+  int   no;            /* atom id */
+  char  name[10];      /* atom name */
+  double x[3];         /* position vector */
+  char  potential[5];  /* atom potential type */
+  char  element[2];    /* atom element */
+  float q;             /* charge */
+  char  residue_string[16]; /* residue string */
+  int  no_connect;	/* number of connections to atom */
+  char connections[MAX_CONNECTIONS][MAX_STRING];  /* long form, connection name*/
+  double bond_order[6];
+  int conn_no[6];	/* Atom number to which atom is connected */
+  int type;
+};
+
+
+_EX  char   rootname[20];
+_EX  char   path[20];
+_EX  double pbc[9];
+_EX  int    periodic   _ARG( 1 ); /* 0= nonperiodic 1= 3-D periodic */
+_EX  int    forcefield _ARG( 0 ); /* 0= ClassI      1= ClassII */
+_EX  int    pflag;
+_EX  int    *no_atoms;
+_EX  int    no_molecules;
+_EX  int    replicate[3];
+_EX  int    total_no_atoms;
+_EX  int    total_no_bonds;
+_EX  int    total_no_angles;
+_EX  int    total_no_dihedrals;
+_EX  int    total_no_angle_angles;
+_EX  int    total_no_oops;
+_EX  int    no_atom_types;
+_EX  int    no_bond_types;
+_EX  int    no_angle_types;
+_EX  int    no_dihedral_types;
+_EX  int    no_oop_types;
+_EX  int    no_angleangle_types;
+_EX  char   FrcFileName[MAX_LINE_LENGTH];
+_EX  FILE   *CarF;
+_EX  FILE   *FrcF;
+_EX  FILE   *PrmF;
+_EX  FILE   *MdfF;
+_EX  FILE   *RptF;
+_EX  struct Atom *atoms;
+_EX  struct MoleculeList *molecule;
+_EX  struct BondList *bonds;
+_EX  struct AngleList *angles;
+_EX  struct DihedralList *dihedrals;
+_EX  struct OOPList *oops;
+_EX  struct AngleAngleList *angleangles;
+_EX  struct AtomTypeList *atomtypes;
+_EX  struct BondTypeList *bondtypes;
+_EX  struct AngleTypeList *angletypes;
+_EX  struct DihedralTypeList *dihedraltypes;
+_EX  struct OOPTypeList *ooptypes;
+_EX  struct AngleAngleTypeList *angleangletypes;
+#undef _EX
+#undef _ARG
+

tools/msi2lmp/src/ReadCarFile.c

@@ -0,0 +1,171 @@
+/*
+*  This function opens the .car file and extracts coordinate information
+*  into the atoms Atom structure
+*/
+
+#include "Msi2LMP2.h"
+
+void ReadCarFile(void)
+{
+   char line[MAX_LINE_LENGTH];  /* Stores lines as they are read in */
+   int k,m,n;			/* counters */	
+   int skip;			/* lines to skip at beginning of file */
+   double  lowest, highest;	/* temp coordinate finding variables */
+   double total_q;
+
+/* Open .car file for reading */
+
+   sprintf(line,"%s.car",rootname);
+   if (pflag > 0) fprintf(stderr," Reading car file: %s\n",line);
+   if( (CarF = fopen(line,"r")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",line);
+      exit(2);
+   }
+
+/* Determine Number of molecules & atoms */
+
+   rewind(CarF);
+   no_molecules = -1; /* Set to -1 because counter will be incremented an
+			 extra time at the end of the file */
+
+   fgets(line,MAX_LINE_LENGTH,CarF); /* Read header line */
+
+/* Check for periodicity, if present, read cell constants */
+
+   if( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"PBC=ON",6) == 0) {
+     periodic = 1;
+     skip = 5; /* Data starts 5 lines from beginning of file */
+     fgets(line,MAX_LINE_LENGTH,CarF); /* Comment line */
+     fgets(line,MAX_LINE_LENGTH,CarF); /* Date stamp */
+      fscanf(CarF,"%*s %lf %lf %lf %lf %lf %lf %*s",
+	     &pbc[0],&pbc[1],&pbc[2],&pbc[3],&pbc[4],&pbc[5]);
+      if(pbc[3] != 90.0 || pbc[4] != 90.0 || pbc[5] != 90.0) {
+         fprintf(stderr,"The system is not rectangular- LAMMPS can't handle it!!");
+         exit(2);
+      }
+   }
+   else {
+      periodic = 0;
+      skip = 4;
+      if (pflag > 1) {
+	fprintf(stderr,"   %s is not a periodic system\n", rootname);
+	fprintf(stderr,"   Assigning cell parameters based on coordinates\n");
+      }
+      fgets(line,MAX_LINE_LENGTH, CarF); /* Comment line */
+      fgets(line,MAX_LINE_LENGTH, CarF); /* Date Stamp */
+   }
+
+/* First pass through file -- Count molecules */
+
+   while(fgets(line,MAX_LINE_LENGTH,CarF) != NULL )
+      if( strncmp(line,"end",3) == 0 )
+         no_molecules++;
+
+/* Allocate space to keep track of the number of atoms within a molecule */
+
+   no_atoms = (int *) calloc(no_molecules,sizeof(int));
+   if ( no_atoms == NULL ) {
+     fprintf(stderr,"Could not allocate memory for no_atoms\n");
+     exit(2);
+   }
+
+/* Second pass through file -- Count atoms */
+
+   rewind(CarF);
+   for(n=0; n < skip; n++)               /* Skip beginning lines */
+     fgets(line,MAX_LINE_LENGTH,CarF);
+   
+   for(n=0; n < no_molecules; n++)
+     while( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"end",3) )
+       no_atoms[n]++;
+
+   for( total_no_atoms=0, n=0; n < no_molecules; n++ )
+     total_no_atoms += no_atoms[n];
+
+   molecule = (struct MoleculeList *) calloc(no_molecules,
+					     sizeof(struct MoleculeList));
+   if (molecule == NULL) {
+     fprintf(stderr,"Unable to allocate memory for molecule structure\n");
+     exit(2);
+   }
+   molecule[0].start = 0;
+   molecule[0].end = no_atoms[0];
+   for (n=1; n < no_molecules; n++) {
+     molecule[n].start = molecule[n-1].end;
+     molecule[n].end = molecule[n].start + no_atoms[n];
+   }
+
+/* Allocate space for atoms Atom structures */
+
+   atoms = (struct Atom *) calloc(total_no_atoms,sizeof(struct Atom));
+   if( atoms == NULL ) {
+     fprintf(stderr,"Could not allocate memory for AtomList\n");
+     exit(2);
+   }
+   
+/* Third pass through file -- Read+Parse Car File */
+
+   rewind(CarF);
+   for(n=0; n < skip; n++)
+     fgets(line,MAX_LINE_LENGTH,CarF);
+
+   for(m=0; m < no_molecules; m++) {
+     for(k=molecule[m].start; k <
+	   molecule[m].end; k++) {
+
+       atoms[k].molecule = m;
+       atoms[k].no = k;
+
+       fscanf(CarF,"%s %lf %lf %lf %*s %*s %s %s %f",
+	      atoms[k].name,
+	      &(atoms[k].x[0]),
+	      &(atoms[k].x[1]),
+	      &(atoms[k].x[2]),
+	      atoms[k].potential,
+	      atoms[k].element,
+	      &(atoms[k].q));
+     }
+     fgets(line,MAX_LINE_LENGTH,CarF);
+     fgets(line,MAX_LINE_LENGTH,CarF);
+
+   } /* End m (molecule) loop */
+
+   for (total_q=0.0,k=0; k < total_no_atoms; k++)
+     total_q += atoms[k].q;
+
+   if (pflag > 1) {
+     fprintf(stderr,"   There are %d atoms in %d molecules in this file\n",
+	     total_no_atoms,no_molecules);
+     fprintf(stderr,"   The total charge in the system is %7.3f.\n\n",total_q);
+   }
+
+/* Search coordinates to find lowest and highest for x, y, and z */
+
+   if (periodic == 0) {
+     for ( k = 0; k < 3; k++) {
+       lowest  = atoms[0].x[k];
+       highest = atoms[0].x[k];
+
+       for ( m = 1; m < total_no_atoms; m++) {
+         if (atoms[m].x[k] < lowest)  lowest = atoms[m].x[k];
+         if (atoms[m].x[k] > highest) highest = atoms[m].x[k];
+       }
+       pbc[k] = lowest;
+       pbc[k+3] = highest;
+     }
+   }
+   else {
+     for (k=0; k < 3; k++) {
+       pbc[k+3] = pbc[k];
+       pbc[k] = 0.0;
+     }
+   }
+
+/* Close .car file */
+   
+   if (fclose(CarF) !=0) {
+      fprintf(stderr,"Error closing %s.car\n", rootname);
+      exit(1);
+   }
+}
+/* End ReadCarFile() */

tools/msi2lmp/src/ReadFrcFile.c

@@ -0,0 +1,88 @@
+/*
+*   This routine reads the data from a .frc forcefield file and stores it in
+*   dynamically allocated memory. This allows for fast searches of the
+*   file.
+*
+*/
+
+#define FF_MAIN
+
+#include "Forcefield.h"
+#include "Msi2LMP2.h"
+
+void ReadFrcFile(void)
+{
+   extern void InitializeItems(void);
+   extern void SearchAndFill(struct FrcFieldItem *item);
+
+  /* Open Forcefield File */
+   if ( (FrcF = fopen(FrcFileName,"r")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n", FrcFileName);
+      exit(2);
+   }
+   InitializeItems(); /* sets keywords, number of members and number of
+			 parameters for each structure */
+  /* allocate memory to and search and fill each structure */
+
+
+   SearchAndFill(&ff_atomtypes);
+   SearchAndFill(&equivalence);
+   SearchAndFill(&ff_vdw);
+   SearchAndFill(&ff_bond);
+   SearchAndFill(&ff_ang);
+   SearchAndFill(&ff_tor);
+   SearchAndFill(&ff_oop);
+   
+   if (forcefield != 1) {  /* Skip cross terms for class I */
+     SearchAndFill(&ff_bonbon);
+     SearchAndFill(&ff_bonang);
+     SearchAndFill(&ff_angtor);
+     SearchAndFill(&ff_angangtor);
+     SearchAndFill(&ff_endbontor);
+     SearchAndFill(&ff_midbontor);
+     SearchAndFill(&ff_bonbon13);
+     SearchAndFill(&ff_angang);
+   }
+   if (pflag > 1) { 
+
+     fprintf(stderr,"\n Item %s has %d entries\n",
+	     ff_atomtypes.keyword,ff_atomtypes.entries);
+     fprintf(stderr," Item %s has %d entries\n",
+	     equivalence.keyword,equivalence.entries);
+     fprintf(stderr," Item %s has %d entries\n",
+	     ff_vdw.keyword,ff_vdw.entries);
+     fprintf(stderr," Item %s has %d entries\n",
+	     ff_bond.keyword,ff_bond.entries);
+     fprintf(stderr," Item %s has %d entries\n",
+	     ff_ang.keyword,ff_ang.entries);
+     if (forcefield > 1) {
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_bonbon.keyword,ff_bonbon.entries);
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_bonang.keyword,ff_bonang.entries);
+     }
+     fprintf(stderr," Item %s has %d entries\n",
+	     ff_tor.keyword,ff_tor.entries);
+     if (forcefield > 1) {
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_angtor.keyword,ff_angtor.entries);
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_angangtor.keyword,ff_angangtor.entries);
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_endbontor.keyword,ff_endbontor.entries);
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_midbontor.keyword,ff_midbontor.entries);
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_bonbon13.keyword,ff_bonbon13.entries);
+     }
+     fprintf(stderr," Item %s has %d entries\n",
+	     ff_oop.keyword,ff_oop.entries);
+     if (forcefield > 1) {
+       fprintf(stderr," Item %s has %d entries\n",
+	       ff_angang.keyword,ff_angang.entries);
+     }
+     fprintf(stderr,"\n");
+   }
+   fclose(FrcF);
+}
+

tools/msi2lmp/src/ReadMdfFile.c

@@ -0,0 +1,425 @@
+/******************************
+*
+*  This function opens the .mdf file and extracts connectivity information
+*  into the atoms Atom structure.  It also updates the charge from the .car
+*  file because the charge in the .mdf file has more significant figures.
+*
+*/
+
+#include "Msi2LMP2.h"
+
+/* Prototype for function to process a single atom
+   Returns int that flags end of data file */
+
+int get_molecule(char line[], int connect_col_no,
+		 int q_col_no, int *counter);
+
+/* Prototype for function that takes connectivty record as stated in
+   .mdf file and fills in any default values */
+void MakeConnectFullForm(int *counter);
+
+/* prototype for function to clean strange characters out of strings */
+
+void clean_string(char *);
+
+void ReadMdfFile(void)
+{
+   char line[MAX_LINE_LENGTH];	/* Temporary storage for reading lines */
+   char *col_no;		/* Pointer to column number stored as char */
+   char *col_name;		/* Pointer to column name */
+   int connect_col_no = 0;	/* Column number where connection info begins */
+   int q_col_no = 0;		/* Column number containg charge information */
+   int column_flag=0;		/* Flag for finding connect and q col no */
+   int atom_counter=0;		/* Keeps track of current atom number */
+   int p_flag = 1; 		/* return value from ProcessConnections() */
+
+   int i,j,k,kk,l,n,match,match2,status;
+   char *temp_string;
+   char *temp_residue;
+   char *temp_atom_name;
+   char *sptr;
+   char *molecule_name;
+   unsigned char at_end = 0;
+
+/* Open .mdf file for reading */
+
+
+   sprintf(line,"%s.mdf",rootname);
+   if (pflag > 0) fprintf(stderr," Reading mdf file: %s\n",line);
+   if ((MdfF = fopen(line,"r")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",line);
+      exit(2);
+   }
+
+   while (!at_end) {
+
+     sptr = fgets(line,MAX_LINE_LENGTH,MdfF);
+
+     if (sptr != NULL) {
+
+       clean_string(line);
+
+       if (strncmp(line,"#end",4) == 0) {
+	 at_end = 1;
+       }
+       else if (strncmp(line,"@column",7) == 0) {
+
+	 temp_string = strtok(line," ");
+	 col_no = strtok(NULL," ");
+	 col_name = strtok(NULL," ");
+	 if (strncmp(col_name,"charge",6) == 0) {
+	   if (strlen(col_name) < 8) {
+	     q_col_no = atoi(col_no);
+	   }
+	 }
+	 else if (strncmp(col_name,"connect",7) == 0) {
+	   connect_col_no = atoi(col_no);
+	 }
+       }
+       else if (strncmp(line,"@molecule",9) == 0) {
+	 temp_string = strtok(line," ");
+	 molecule_name = strtok(NULL," ");
+
+	 if ((q_col_no == 0) | (connect_col_no == 0)) {
+	   fprintf(stderr,"Unable to process molecule without knowing charge\n");
+	   fprintf(stderr,"and connections columns\n");
+	 }
+	 sptr = fgets(line,MAX_LINE_LENGTH,MdfF);
+	 status = get_molecule(line,connect_col_no,q_col_no,&atom_counter);
+	 if (status == 0) {
+	   fprintf(stderr,"Trouble reading molecule - exiting\n");
+	 }
+       }
+       else {
+       }
+     }
+     else {
+       fprintf(stderr,"End of File found or error reading line\n");
+       at_end = 1;
+     }
+   }
+
+   /* Next build list of residues for each molecule This will
+      facilitate assigning connections numbers as well as figuring
+      out bonds, angles, etc.  This first loop just figures out the
+      number of residues in each molecule and allocates memory to
+      store information for each residue. The second loop fills
+      in starting and ending atom positions for each residue
+   */
+
+   temp_string = calloc(16,sizeof(char));
+   temp_string[15] = '\0';
+
+   for (n=0; n < no_molecules; n++) {
+     molecule[n].no_residues = 1;
+
+     strncpy(temp_string,atoms[molecule[n].start].residue_string,16);
+     for (i=molecule[n].start+1; i < molecule[n].end; i++) {
+       if (strncmp(temp_string,atoms[i].residue_string,16) != 0) {
+	 molecule[n].no_residues++;
+	 strncpy(temp_string,atoms[i].residue_string,16);
+       }
+     }
+
+     molecule[n].residue = (struct ResidueList *) 
+       calloc(molecule[n].no_residues, sizeof(struct ResidueList));
+
+     if (molecule[n].residue == NULL) {
+       fprintf(stderr,"Unable to allocate memory for residue list - molecule %d\n",
+	      n);
+       exit(1);
+     }
+   }
+   for (n=0; n < no_molecules; n++) {
+     j = 0;
+     strncpy(molecule[n].residue[j].name,
+	atoms[molecule[n].start].residue_string,16);
+
+     molecule[n].residue[j].start = molecule[n].start;
+     for (i=molecule[n].start+1; i < molecule[n].end; i++) {
+       if (strncmp(molecule[n].residue[j].name,
+		  atoms[i].residue_string,16) != 0) {
+	
+	 molecule[n].residue[j].end = i;
+	 molecule[n].residue[++j].start = i;
+	 strncpy(molecule[n].residue[j].name,atoms[i].residue_string,16);
+       }
+     }
+     molecule[n].residue[j].end = molecule[n].end;
+       /*
+       fprintf(stderr,"Molecule %d has %d residues",n,molecule[n].no_residues);
+       for (i=0; i < molecule[n].no_residues; i++) {
+	 fprintf(stderr," %s",molecule[n].residue[i].name);
+       }
+       fprintf(stderr,"\n");
+       for (i=molecule[n].start; i < molecule[n].end; i++) {
+	 fprintf(stderr," atom %d residue %s\n",i,atoms[i].residue_string);
+       }
+       fprintf(stderr," residue %s start %d end %d\n",molecule[n].residue[i].name,
+	molecule[n].residue[i].start,molecule[n].residue[i].end);
+       }
+       */
+   }
+
+   /* Assign atom names in connections[] to corresponding atom numbers */
+
+   for (n=0; n < no_molecules; n++) {
+     for (j=0; j < molecule[n].no_residues; j++) {
+       for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end;
+	    i++) {
+	 for (l=0; l < atoms[i].no_connect; l++) {
+	   strncpy(temp_string,atoms[i].connections[l],16);
+	   temp_residue = strtok(temp_string,":");
+	   temp_atom_name = strtok(NULL,"%");
+
+	   if (strcmp(temp_residue,molecule[n].residue[j].name) == 0) {
+
+	     /* atom and connection are part of same residue
+	        Search names on just that residue            */
+
+	     k = molecule[n].residue[j].start;
+	     match = 0;
+	     while (!match && (k < molecule[n].residue[j].end)) {
+	       if (strcmp(atoms[k].name,temp_atom_name) == 0) {
+		 atoms[i].conn_no[l] = k;
+		 match = 1;
+	       }
+	       else
+		 k++;
+	     }
+	     if (match == 0) {
+	       fprintf(stderr,"Unable to resolve atom number of atom %d conn %d string %s:%s\n Something is wrong in the MDF file\n",
+		      i,l,temp_residue,temp_atom_name);
+	       exit(1);
+	     }
+	   }
+	   else {
+
+	     /* atom and connection are on different residues
+	        First find the residue that the connection is
+		on then loop over its atoms
+	     */
+
+	     k=0;
+	     match = 0;
+	     while (!match && (k < molecule[n].no_residues)) {
+	       if (strcmp(temp_residue,molecule[n].residue[k].name) == 0) {
+		 kk = molecule[n].residue[k].start;
+		 match2 = 0;
+		 while (!match2 && (kk < molecule[n].residue[k].end)) {
+		   if (strcmp(atoms[kk].name,temp_atom_name) == 0) {
+		     atoms[i].conn_no[l] = kk;
+		     match2 = 1;
+		   }
+		   else
+		     kk++;
+		 }
+		 if (match2 == 0) {
+		   fprintf(stderr,"Unable to resolve atom number of atom %d conn %d string %s\n Something is wrong in the MDF file\n",
+			  i,l,atoms[i].connections[l]);
+		   exit(1);
+		 }
+		 match = 1;
+	       }
+	       else
+		 k++;
+	     }
+	     if (match == 0) {
+	       fprintf(stderr,"Unable to find residue associated with conn %d %s on atom %d\n Something is wrong in the MDF file\n", l,atoms[i].connections[l],i);
+	       exit(1);
+	     }
+	   } /* end if */
+	 } /* l - loop over connections on atom i */
+	 
+       } /* i - loop on atoms in residue j molecule n */
+       
+     } /* j - loop on residues in molecule n */
+     
+   } /* n - loop over molecules */
+
+   free(temp_string);
+   /*
+   for (n=0; n < no_molecules; n++) {
+
+   fprintf(stderr,"Molecule %d has %d residues\n",n,molecule[n].no_residues);
+     for (j=0; j < molecule[n].no_residues; j++) {
+       fprintf(stderr," Residue %d named %s\n",j,molecule[n].residue[j].name);
+       for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end;
+	    i++) {
+	    fprintf(stderr,"  Atom %d type %s connected to ",i,atoms[i].potential);
+	 for (l=0; l < atoms[i].no_connect; l++) fprintf(stderr," %d ",
+	 atoms[i].conn_no[l]);
+	 fprintf(stderr,"\n");
+       }
+     }
+   }
+
+*/
+
+/* Close .mdf file */
+
+   if (fclose(MdfF) !=0) {
+     printf("Error closing %s.car\n", rootname);
+     exit(1);
+   }
+   
+} /* End ReadMdfFile function */
+
+/*--------------------- get_molecule Function-----------------------*/
+
+int get_molecule(char *line, int connect_col_no, int q_col_no,
+		 int *counter)
+{
+  char *cur_field;	/* For storing current string token */
+  int i; 		/* Used in loop counters */
+  int connect_no;      /* Connection number within atom */
+  int r_val = 1;	/* Return value.  1 = successful
+					  0 = EOF encountered */
+ /* Loop over atoms */
+
+  /* blank line signals end of molecule*/
+  while(!blank_line(fgets(line,MAX_LINE_LENGTH,MdfF))) {
+    /*  while(strlen(fgets(line,MAX_LINE_LENGTH,MdfF)) > 2) { */
+
+      clean_string(line);
+
+    /* Get atom name */
+    cur_field = strtok(line,":");
+    sscanf(cur_field, "%s", atoms[*counter].residue_string);
+    cur_field = strtok(NULL," "); 
+    /* Compare atom name with that in .car file */
+    if (strcmp(atoms[*counter].name, cur_field)) {
+      fprintf(stderr,"Names %s from .car file and %s from .mdf file do not match\n",
+	      atoms[*counter].name, cur_field);
+      fprintf(stderr,"counter = %d\n",*counter);
+      fprintf(stderr,"Program Terminating\n");
+      exit(4);
+    }
+
+  /* Skip unwanted fields until charge column, then update charge */
+    
+    for (i=1; i < q_col_no; i++) strtok(NULL," ");
+    cur_field = strtok(NULL, " ");
+    atoms[*counter].q = atof(cur_field);
+
+  /* Continue skipping unwanted fields until connectivity records begin */
+
+    for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL," ");
+
+   /* Process connections */
+
+    connect_no = 0; /* reset connections counter */
+    while ((cur_field = strtok(NULL," ")) && (connect_no < MAX_CONNECTIONS)) {
+      sscanf(cur_field, "%s", atoms[*counter].connections[connect_no++]);
+    }
+    atoms[*counter].no_connect = connect_no;
+    MakeConnectFullForm(counter);
+    (*counter)++;
+
+   } /* End atom processing loop */
+
+   return r_val;
+
+} /* End get_molecule function */
+
+
+
+ /*------------------------MakeConnectFullForm Function--------------------*/
+
+void MakeConnectFullForm(int *counter) {
+
+  /* This function processes the connection names after all connections
+   for an atom have been read in.
+   It replaces any short forms that use implied default values
+   with the full form connectivity record */
+
+   int i;		/* Counter for character array */
+   int j;		/* loop counter */
+   char tempname[MAX_STRING];   /* name of connection */
+   char tempcell[10];   /* Values from connectivity record */
+   char tempsym[5];              /* " " */
+   char tempbo[6];               /* " " */
+   char *charptr;
+
+   for ( j = 0; j < atoms[*counter].no_connect; j++) {
+  /* If not full name, make name full */
+     if (strchr(atoms[*counter].connections[j],':') == NULL) {
+         strcpy(tempname,atoms[*counter].residue_string);
+	 strcat(tempname,":");
+         strcat(tempname,
+		atoms[*counter].connections[j]);
+         sscanf(tempname, "%s",
+		atoms[*counter].connections[j]);
+     }
+     else
+       sscanf(atoms[*counter].connections[j], "%s", tempname);
+     /* Set cell variables */
+     
+     i=0;
+     charptr = (strchr(tempname,'%'));
+     if (charptr != NULL) {
+       while ( *charptr!='#' && *charptr!='/' && *charptr!='\000')
+         tempcell[i++] = *(charptr++);
+       tempcell[i] = '\000';
+     }
+     else
+       strcpy(tempcell, "%000");
+
+  /* Set symmetry variables
+	-- If not 1, cannot handle at this time */
+
+   i = 0;
+   charptr = (strchr(tempname,'#'));
+   if (charptr != NULL)  {
+     while (*charptr != '/' && *charptr !='\000') {
+       tempsym[i++] = *(charptr++);
+          if ((i==2) && (tempsym[1] != '1')) {
+	    fprintf(stderr,"Msi2LMP is not equipped to handle symmetry operations\n");
+	    exit(5);
+          }
+       }
+     tempsym[i] = '\000';
+   }
+   else
+     strcpy(tempsym, "#1");
+
+  /* Set bond order and record in data structure */
+
+   i = 0;
+   charptr = strchr(tempname,'/');
+   if (charptr != NULL) {
+      charptr++;
+      while (*charptr != '\000')
+	tempbo[i++] = *(charptr++);
+      tempbo[i] = '\000';
+   }
+   else
+     strcpy(tempbo, "1.0");
+
+   atoms[*counter].bond_order[j] = atof(tempbo);
+
+/* Build connection name and store in atoms data structure */
+
+    strtok( tempname, "%#/");
+    strcat( tempname, tempcell);
+    strcat( tempname, tempsym);
+    strcat( tempname, "/");
+    strcat( tempname, tempbo);
+    if (strlen(tempname) > 25) fprintf(stderr,"tempname overrun %s\n",tempname);
+    sscanf( tempname, "%s", atoms[*counter].connections[j]);
+   }/*End for loop*/
+}/* End function MakeNameLong
+*/
+
+void clean_string(char *string) {
+  int i,n;
+  short k;
+
+  n = strlen(string);
+  for (i=0; i < n; i++) {
+    k = (short)string[i];
+    if ((k<32) | (k>127)) string[i] = '\0';
+  }
+}
+
+

tools/msi2lmp/src/SearchAndFill.c

@@ -0,0 +1,218 @@
+/****************************
+*
+* This function first allocates memory to the forcefield item
+* structures and then reads parameters from the forcefield file into the
+* allocated memory
+*
+*/
+
+#include "Forcefield.h"
+#include "Msi2LMP2.h"
+
+unsigned char string_match(char *,char *);
+
+void SearchAndFill(struct FrcFieldItem *item)
+{
+   int i,j;  /* counters */
+   int got_it = 0;
+   int ctr = 0;
+   long file_pos;
+   char line[MAX_LINE] = "empty";
+   char *charptr,*status;
+   extern FILE *FrcF;
+
+
+   /***********************ALLOCATE MEMORY FOR STRUCTURE ********************/
+
+   /* Read and discard lines until keyword is found */
+
+   rewind(FrcF);
+   while ((got_it == 0)) {
+     status = fgets( line, MAX_LINE, FrcF );
+     if (status == NULL) {
+       fprintf(stderr," Unable to find forcefield keyword %s\n",item->keyword);
+       fprintf(stderr," Check consistency of forcefield name and class \n");
+       fprintf(stderr," Exiting....\n");
+       exit(1);
+     }
+     if (line[0] == '#') {
+       if (string_match(strtok(line," '\t'("),item->keyword)) got_it = 1;
+     }
+     /*     if (strncmp(line, item->keyword,strlen(item->keyword))==0) got_it = 1; */
+   }
+
+   file_pos = ftell(FrcF);
+
+   /* Count the number of lines until next item is found */
+
+   while( strncmp(fgets(line,MAX_LINE,FrcF), "#", 1) != 0 )
+     ctr++;
+
+   /* Allocate the memory using calloc */
+
+   item->data = calloc(ctr, sizeof(struct FrcFieldData));
+
+   if (item->data == NULL) {
+     fprintf(stderr,"Could not allocate memory to %s\n", item->keyword);
+     exit(2);
+   }
+
+   /********************FILL PARAMETERS AND EQUIVALENCES ********************/
+
+   /* Read lines until keyword is found */
+
+   fseek(FrcF,file_pos,SEEK_SET);
+   strcpy(line,"empty");
+
+   /* Read lines until data starts (when !--- is found) */
+
+   ctr = 0;
+   while ( strncmp(line,"!---", 4) != 0 ) {
+      fgets(line, MAX_LINE, FrcF);
+   }
+
+   /* Get first line of data that isn't commented out */
+
+   fgets(line, MAX_LINE, FrcF); 
+   while (strncmp(line,"!",1) == 0) {
+     fgets( line, MAX_LINE, FrcF);
+   }
+
+   /* Read data into structure */
+
+   while( strncmp( line, "#", 1 ) != 0 ) {
+
+     float version;
+     int reference,replace;
+     char atom_types[5][5];
+     double parameters[8];
+
+     /* version number and reference number */
+
+     version = atof(strtok(line, " "));
+     reference = atoi(strtok(NULL, " "));
+
+     /* equivalences */
+
+     for(i = 0; i < item->number_of_members; i++ ) {
+       sscanf(strtok(NULL, " "), "%s", atom_types[i]);
+     }
+
+     /* parameters -- Because of symmetrical terms, bonang, angtor, and
+	endbontor have to be treated carefully */
+
+     for( i = 0; i < item->number_of_parameters; i++ ) {
+       charptr = strtok(NULL, " ");
+       if(charptr == NULL) {
+	 for ( j = i; j < item->number_of_parameters; j++ )
+	   parameters[j] = parameters[j-i];
+	 break;
+       }
+       else {
+	 parameters[i] = atof(charptr);
+       }
+     }
+     /* Search for matching sets of atom types.
+	If found and the version number is greater, substitute 
+	the current set of parameters in place of the found set. 
+	Otherwise, add the current set of parameters to the 
+	list. 
+     */
+     replace = ctr;
+     for (j=0; j < ctr; j++) {
+	 
+       int k=0;
+       int match = 1;
+       while (match && (k < item->number_of_members)) {
+	 if (strncmp(item->data[j].ff_types[k],atom_types[k],5) == 0)
+	   k++;
+	 else
+	   match = 0;
+       }
+       if (match == 1) {
+	 replace = j;
+	 break;
+       }
+     }
+     if (replace != ctr) {
+       if (version > item->data[replace].ver) { 
+
+	 if (pflag > 1) {
+	   fprintf(stderr," Using higher version of parameters for");
+	   fprintf(stderr," %s  ",item->keyword);
+	   for (i=0; i < item->number_of_members; i++) 
+	     fprintf(stderr,"%s ",atom_types[i]);
+	   fprintf(stderr," version %3.2f\n",version);
+	 }
+							     
+	 item->data[replace].ver = version;
+	 item->data[replace].ref = reference;
+	 for (i=0; i < item->number_of_members; i++) {
+	   strncpy(item->data[replace].ff_types[i],atom_types[i],5);
+	 }
+	 for (i=0; i < item->number_of_parameters; i++) {
+	   item->data[replace].ff_param[i] = parameters[i];
+	 }
+       }
+       else {
+	 if (pflag > 1) {
+	   fprintf(stderr," Using higher version of parameters for");
+	   fprintf(stderr," %s  ",item->keyword);
+	   for (i=0; i < item->number_of_members; i++) 
+	     fprintf(stderr,"%s ",item->data[replace].ff_types[i]);
+	   fprintf(stderr," version %3.2f\n",item->data[replace].ver);
+	 }
+       }
+     }
+     else {
+       item->data[ctr].ver = version;
+       item->data[ctr].ref = reference;
+       for (i=0; i < item->number_of_members; i++) {
+	 strncpy(item->data[ctr].ff_types[i],atom_types[i],5);
+       }
+       for (i=0; i < item->number_of_parameters; i++) {
+	 item->data[ctr].ff_param[i] = parameters[i];
+       }
+       ctr++;
+     }
+     fgets( line, MAX_LINE, FrcF);
+     /*if blank line encountered, get next */
+     while((blank_line(line)) ||
+	   (strncmp(line,"!",1) == 0)) {
+       fgets( line, MAX_LINE, FrcF);
+     }
+   }
+   item->entries = ctr; 
+
+   /*Debugging
+     fprintf(stderr,"\n%s\n", item->keyword);
+     for(i=0;i<ctr;i++) {
+     for(j=0;j<item->number_of_members;j++)
+     fprintf(stderr,"%3s ", item->data[i].ff_equiv[j]);
+     fprintf(stderr,"     ");
+     for(j=0;j<item->number_of_parameters;j++)
+     fprintf(stderr,"%10.5f ",item->data[i].ff_param[j]);
+     fprintf(stderr,"\n");
+     }
+   */
+}
+
+unsigned char string_match(char *string1,char *string2)
+{
+  int len1,len2;
+
+  len1 = strlen(string1);
+  len2 = strlen(string2);
+
+  if (len1 != len2) {
+    return 0;
+  }
+  else {
+    if (strncmp(string1,string2,len1) == 0) {
+      return 1;
+    }
+    else { 
+      return 0;
+    }
+  }
+}

tools/msi2lmp/src/WriteDataFile.c

@@ -0,0 +1,313 @@
+/*
+*  This function creates and writes the data file to be used with LAMMPS
+*/
+
+#include "Msi2LMP2.h"
+#include "Forcefield.h"
+
+void WriteDataFile(FILE *DatF,char *nameroot,int forcefield)
+{
+   int i,j,k,m;
+   char line[MAX_LINE_LENGTH];
+
+   if (forcefield == 1) total_no_angle_angles = 0;
+
+   fprintf(DatF, "LAMMPS data file for %s\n\n", nameroot);
+   fprintf(DatF, " %6d atoms\n", total_no_atoms);
+   fprintf(DatF, " %6d bonds\n", total_no_bonds);
+   fprintf(DatF, " %6d angles\n",total_no_angles);
+   fprintf(DatF, " %6d dihedrals\n", total_no_dihedrals);
+   fprintf(DatF, " %6d impropers\n", total_no_oops+total_no_angle_angles);
+   fprintf(DatF, "\n");
+
+
+   fprintf(DatF, " %3d atom types\n", no_atom_types);
+   if (no_bond_types > 0)
+     fprintf(DatF, " %3d bond types\n", no_bond_types);
+   if (no_angle_types> 0)
+     fprintf(DatF, " %3d angle types\n", no_angle_types);
+   if (no_dihedral_types > 0) fprintf  (DatF," %3d dihedral types\n",
+					no_dihedral_types);
+   if (forcefield > 1) {
+     if ((no_oop_types + no_angleangle_types) > 0)
+       fprintf  (DatF, " %3d improper types\n", 
+		 no_oop_types + no_angleangle_types);
+   }
+   else {
+     if (no_oop_types > 0)
+       fprintf  (DatF, " %3d improper types\n", no_oop_types);
+   }
+
+   fprintf(DatF, "\n");
+   fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
+   fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
+   fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
+
+   /* MASSES */
+
+
+   fprintf(DatF, "\nMasses\n\n");
+   for(k=0; k < no_atom_types; k++)
+     fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
+   fprintf(DatF, "\n");
+
+
+   /* COEFFICIENTS */
+
+   fprintf(DatF,"Nonbond Coeffs\n\n");
+   for (i=0; i < no_atom_types; i++) {
+     fprintf(DatF, " %3i ", i+1);
+     for ( j = 0; j < 2; j++)
+       fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
+     fprintf(DatF, "\n");
+   }
+   fprintf(DatF, "\n");
+
+   if (no_bond_types > 0) {
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Bond Coeffs\n\n");
+     for (i=0; i < no_bond_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_angle_types > 0) {
+
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Angle Coeffs\n\n");
+     for (i=0; i < no_angle_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	
+	 fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_dihedral_types > 0) {
+     if (forcefield == 1) m = 3;
+     if (forcefield == 2) m = 6;
+
+     fprintf(DatF,"Dihedral Coeffs\n\n");
+     for (i=0; i < no_dihedral_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+   if (forcefield == 1) {
+     if (no_oop_types > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   else if (forcefield == 2) {
+     if ((no_oop_types + no_angleangle_types) > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", 0.0);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   if (forcefield == 2) {
+
+     if (no_angle_types > 0) {
+       fprintf(DatF,"BondBond Coeffs\n\n");
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", angletypes[i].bondbond_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"BondAngle Coeffs\n\n");
+
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF, "%10.4f ",angletypes[i].bondangle_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if ((no_oop_types+no_angleangle_types) > 0) {
+       fprintf(DatF,"AngleAngle Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].angleangle_params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", angleangletypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if (no_dihedral_types > 0) {
+       fprintf(DatF,"AngleAngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].angleangledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"EndBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ", 
+		   dihedraltypes[i].endbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"MiddleBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].midbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+
+       fprintf(DatF,"BondBond13 Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].bond13_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"AngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].angledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+
+   /*--------------------------------------------------------------------*/
+
+   /* ATOMS */
+
+   fprintf(DatF, "Atoms\n\n");
+   for(k=0; k < total_no_atoms; k++) {
+      fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f\n",
+              k+1,
+              atoms[k].molecule,
+	      atoms[k].type+1,
+              atoms[k].q,
+              atoms[k].x[0],
+	      atoms[k].x[1],
+              atoms[k].x[2]);
+   }
+   fprintf(DatF, "\n");
+
+   /***** BONDS *****/
+
+   if (total_no_bonds > 0) {
+     fprintf(DatF, "Bonds\n\n");
+     for(k=0; k < total_no_bonds; k++)
+       fprintf(DatF, "%6i %3i %6i %6i\n",k+1,
+	       bonds[k].type+1,
+	       bonds[k].members[0]+1,
+	       bonds[k].members[1]+1);
+     fprintf(DatF,"\n");
+   }
+
+   /***** ANGLES *****/
+
+   if (total_no_angles > 0) {
+     fprintf(DatF, "Angles\n\n");
+     for(k=0; k < total_no_angles; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i\n",k+1,
+	       angles[k].type+1,
+	       angles[k].members[0]+1,
+	       angles[k].members[1]+1,
+	       angles[k].members[2]+1);
+     fprintf(DatF, "\n");
+   }
+
+
+   /***** TORSIONS *****/
+
+   if (total_no_dihedrals > 0)   {
+      fprintf(DatF,"Dihedrals\n\n");
+      for(k=0; k < total_no_dihedrals; k++)
+	fprintf(DatF, "%6i %3i %6i %6i %6i %6i\n",k+1,
+		dihedrals[k].type+1,
+		dihedrals[k].members[0]+1,
+		dihedrals[k].members[1]+1,
+		dihedrals[k].members[2]+1,
+		dihedrals[k].members[3]+1);
+      fprintf(DatF, "\n");
+   }
+
+   /***** OUT-OF-PLANES *****/
+
+   if (total_no_oops+total_no_angle_angles > 0) {
+     fprintf(DatF,"Impropers\n\n");
+     for (k=0; k < total_no_oops; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n", k+1,
+	       oops[k].type+1,
+	       oops[k].members[0]+1,
+	       oops[k].members[1]+1,
+	       oops[k].members[2]+1,
+	       oops[k].members[3]+1);
+     if (forcefield == 2) {
+       for (k=0; k < total_no_angle_angles; k++)
+	 fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n",k+total_no_oops+1,
+		 angleangles[k].type+no_oop_types+1,
+		 angleangles[k].members[0]+1,
+		 angleangles[k].members[1]+1,
+		 angleangles[k].members[2]+1,
+		 angleangles[k].members[3]+1);
+     }
+     fprintf(DatF, "\n");
+   }
+
+}

tools/msi2lmp/src/WriteDataFile01.c

@@ -0,0 +1,332 @@
+/*
+*  This function creates and writes the data file to be used with LAMMPS
+*/
+
+#include "Msi2LMP2.h"
+#include "Forcefield.h"
+
+void WriteDataFile01(char *nameroot,int forcefield)
+{
+   int i,j,k,m;
+   char line[MAX_LINE_LENGTH];
+   FILE *DatF;
+
+/* Open data file */
+
+   sprintf(line,"%s.lammps01",rootname);
+   if (pflag > 0) fprintf(stderr," Writing LAMMPS 2001 data file: %s\n",line);
+   if( (DatF = fopen(line,"w")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",line);
+      exit(2);
+   }
+
+
+
+   if (forcefield == 1) total_no_angle_angles = 0;
+
+   fprintf(DatF, "LAMMPS data file for %s\n\n", nameroot);
+   fprintf(DatF, " %6d atoms\n", total_no_atoms);
+   fprintf(DatF, " %6d bonds\n", total_no_bonds);
+   fprintf(DatF, " %6d angles\n",total_no_angles);
+   fprintf(DatF, " %6d dihedrals\n", total_no_dihedrals);
+   fprintf(DatF, " %6d impropers\n", total_no_oops+total_no_angle_angles);
+   fprintf(DatF, "\n");
+
+
+   fprintf(DatF, " %3d atom types\n", no_atom_types);
+   if (no_bond_types > 0)
+     fprintf(DatF, " %3d bond types\n", no_bond_types);
+   if (no_angle_types> 0)
+     fprintf(DatF, " %3d angle types\n", no_angle_types);
+   if (no_dihedral_types > 0) fprintf  (DatF," %3d dihedral types\n",
+					no_dihedral_types);
+   if (forcefield > 1) {
+     if ((no_oop_types + no_angleangle_types) > 0)
+       fprintf  (DatF, " %3d improper types\n", 
+		 no_oop_types + no_angleangle_types);
+   }
+   else {
+     if (no_oop_types > 0)
+       fprintf  (DatF, " %3d improper types\n", no_oop_types);
+   }
+
+   fprintf(DatF, "\n");
+   fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
+   fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
+   fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
+
+   /* MASSES */
+
+
+   fprintf(DatF, "\nMasses\n\n");
+   for(k=0; k < no_atom_types; k++)
+     fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
+   fprintf(DatF, "\n");
+
+
+   /* COEFFICIENTS */
+
+   fprintf(DatF,"Nonbond Coeffs\n\n");
+   for (i=0; i < no_atom_types; i++) {
+     fprintf(DatF, " %3i ", i+1);
+     for ( j = 0; j < 2; j++)
+       fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
+     fprintf(DatF, "\n");
+   }
+   fprintf(DatF, "\n");
+
+   if (no_bond_types > 0) {
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Bond Coeffs\n\n");
+     for (i=0; i < no_bond_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_angle_types > 0) {
+
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Angle Coeffs\n\n");
+     for (i=0; i < no_angle_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	
+	 fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_dihedral_types > 0) {
+     if (forcefield == 1) m = 3;
+     if (forcefield == 2) m = 6;
+
+     fprintf(DatF,"Dihedral Coeffs\n\n");
+     for (i=0; i < no_dihedral_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+   if (forcefield == 1) {
+     if (no_oop_types > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   else if (forcefield == 2) {
+     if ((no_oop_types + no_angleangle_types) > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", 0.0);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   if (forcefield == 2) {
+
+     if (no_angle_types > 0) {
+       fprintf(DatF,"BondBond Coeffs\n\n");
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", angletypes[i].bondbond_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"BondAngle Coeffs\n\n");
+
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF, "%10.4f ",angletypes[i].bondangle_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if ((no_oop_types+no_angleangle_types) > 0) {
+       fprintf(DatF,"AngleAngle Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].angleangle_params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", angleangletypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if (no_dihedral_types > 0) {
+       fprintf(DatF,"AngleAngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].angleangledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"EndBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ", 
+		   dihedraltypes[i].endbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"MiddleBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].midbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+
+       fprintf(DatF,"BondBond13 Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].bond13_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"AngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].angledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+
+   /*--------------------------------------------------------------------*/
+
+   /* ATOMS */
+
+   fprintf(DatF, "Atoms\n\n");
+   for(k=0; k < total_no_atoms; k++) {
+      fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f\n",
+              k+1,
+              atoms[k].molecule,
+	      atoms[k].type+1,
+              atoms[k].q,
+              atoms[k].x[0],
+	      atoms[k].x[1],
+              atoms[k].x[2]);
+   }
+   fprintf(DatF, "\n");
+
+   /***** BONDS *****/
+
+   if (total_no_bonds > 0) {
+     fprintf(DatF, "Bonds\n\n");
+     for(k=0; k < total_no_bonds; k++)
+       fprintf(DatF, "%6i %3i %6i %6i\n",k+1,
+	       bonds[k].type+1,
+	       bonds[k].members[0]+1,
+	       bonds[k].members[1]+1);
+     fprintf(DatF,"\n");
+   }
+
+   /***** ANGLES *****/
+
+   if (total_no_angles > 0) {
+     fprintf(DatF, "Angles\n\n");
+     for(k=0; k < total_no_angles; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i\n",k+1,
+	       angles[k].type+1,
+	       angles[k].members[0]+1,
+	       angles[k].members[1]+1,
+	       angles[k].members[2]+1);
+     fprintf(DatF, "\n");
+   }
+
+
+   /***** TORSIONS *****/
+
+   if (total_no_dihedrals > 0)   {
+      fprintf(DatF,"Dihedrals\n\n");
+      for(k=0; k < total_no_dihedrals; k++)
+	fprintf(DatF, "%6i %3i %6i %6i %6i %6i\n",k+1,
+		dihedrals[k].type+1,
+		dihedrals[k].members[0]+1,
+		dihedrals[k].members[1]+1,
+		dihedrals[k].members[2]+1,
+		dihedrals[k].members[3]+1);
+      fprintf(DatF, "\n");
+   }
+
+   /***** OUT-OF-PLANES *****/
+
+   if (total_no_oops+total_no_angle_angles > 0) {
+     fprintf(DatF,"Impropers\n\n");
+     for (k=0; k < total_no_oops; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n", k+1,
+	       oops[k].type+1,
+	       oops[k].members[0]+1,
+	       oops[k].members[1]+1,
+	       oops[k].members[2]+1,
+	       oops[k].members[3]+1);
+     if (forcefield == 2) {
+       for (k=0; k < total_no_angle_angles; k++)
+	 fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n",k+total_no_oops+1,
+		 angleangles[k].type+no_oop_types+1,
+		 angleangles[k].members[0]+1,
+		 angleangles[k].members[1]+1,
+		 angleangles[k].members[2]+1,
+		 angleangles[k].members[3]+1);
+     }
+     fprintf(DatF, "\n");
+   }
+
+/* Close data file */
+
+   if (fclose(DatF) !=0) {
+      fprintf(stderr,"Error closing %s.lammps01\n", rootname);
+      exit(1);
+   }
+
+}

tools/msi2lmp/src/WriteDataFile05.c

@@ -0,0 +1,333 @@
+/*
+*  This function creates and writes the data file to be used with LAMMPS
+*/
+
+#include "Msi2LMP2.h"
+#include "Forcefield.h"
+
+void WriteDataFile05(char *nameroot,int forcefield)
+{
+   int i,j,k,m;
+   char line[MAX_LINE_LENGTH];
+   FILE *DatF;
+
+/* Open data file */
+
+   sprintf(line,"%s.lammps05",rootname);
+   if (pflag > 0) fprintf(stderr," Writing LAMMPS 2005 data file: %s\n",line);
+   if( (DatF = fopen(line,"w")) == NULL ) {
+      fprintf(stderr,"Cannot open %s\n",line);
+      exit(2);
+   }
+
+
+
+   if (forcefield == 1) total_no_angle_angles = 0;
+
+   fprintf(DatF, "LAMMPS 2005 data file for %s\n\n", nameroot);
+   fprintf(DatF, " %6d atoms\n", total_no_atoms);
+   fprintf(DatF, " %6d bonds\n", total_no_bonds);
+   fprintf(DatF, " %6d angles\n",total_no_angles);
+   fprintf(DatF, " %6d dihedrals\n", total_no_dihedrals);
+   fprintf(DatF, " %6d impropers\n", total_no_oops+total_no_angle_angles);
+   fprintf(DatF, "\n");
+
+
+   fprintf(DatF, " %3d atom types\n", no_atom_types);
+   if (no_bond_types > 0)
+     fprintf(DatF, " %3d bond types\n", no_bond_types);
+   if (no_angle_types> 0)
+     fprintf(DatF, " %3d angle types\n", no_angle_types);
+   if (no_dihedral_types > 0) fprintf  (DatF," %3d dihedral types\n",
+					no_dihedral_types);
+   if (forcefield > 1) {
+     if ((no_oop_types + no_angleangle_types) > 0)
+       fprintf  (DatF, " %3d improper types\n", 
+		 no_oop_types + no_angleangle_types);
+   }
+   else {
+     if (no_oop_types > 0)
+       fprintf  (DatF, " %3d improper types\n", no_oop_types);
+   }
+
+   fprintf(DatF, "\n");
+   fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
+   fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
+   fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
+
+   /* MASSES */
+
+
+   fprintf(DatF, "\nMasses\n\n");
+   for(k=0; k < no_atom_types; k++)
+     fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
+   fprintf(DatF, "\n");
+
+
+   /* COEFFICIENTS */
+
+   fprintf(DatF,"Pair Coeffs\n\n");
+   for (i=0; i < no_atom_types; i++) {
+     fprintf(DatF, " %3i ", i+1);
+     for ( j = 0; j < 2; j++)
+       fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
+     fprintf(DatF, "\n");
+   }
+   fprintf(DatF, "\n");
+
+   if (no_bond_types > 0) {
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Bond Coeffs\n\n");
+     for (i=0; i < no_bond_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_angle_types > 0) {
+
+     if (forcefield == 1) m = 2;
+     if (forcefield == 2) m = 4;
+
+     fprintf(DatF,"Angle Coeffs\n\n");
+     for (i=0; i < no_angle_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	
+	 fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+
+   if (no_dihedral_types > 0) {
+     if (forcefield == 1) m = 3;
+     if (forcefield == 2) m = 6;
+
+     fprintf(DatF,"Dihedral Coeffs\n\n");
+     for (i=0; i < no_dihedral_types; i++) {
+       fprintf(DatF, "%3i ", i+1);
+       for ( j = 0; j < m; j++)
+	 fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
+       fprintf(DatF,"\n");
+     }
+     fprintf(DatF, "\n");
+   }
+   if (forcefield == 1) {
+     if (no_oop_types > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   else if (forcefield == 2) {
+     if ((no_oop_types + no_angleangle_types) > 0) {
+       fprintf(DatF,"Improper Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 2; j++)
+	   fprintf(DatF, "%10.4f ", 0.0);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+   if (forcefield == 2) {
+
+     if (no_angle_types > 0) {
+       fprintf(DatF,"BondBond Coeffs\n\n");
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ", angletypes[i].bondbond_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"BondAngle Coeffs\n\n");
+
+       for (i=0; i < no_angle_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF, "%10.4f ",angletypes[i].bondangle_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if ((no_oop_types+no_angleangle_types) > 0) {
+       fprintf(DatF,"AngleAngle Coeffs\n\n");
+       for (i=0; i < no_oop_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", ooptypes[i].angleangle_params[j]);
+	 fprintf(DatF, "\n");
+       }
+       for (i=0; i < no_angleangle_types; i++) {
+	 fprintf(DatF, "%3i ", i+no_oop_types+1);
+	 for ( j = 0; j < 6; j++)
+	   fprintf(DatF, "%10.4f ", angleangletypes[i].params[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+
+     if (no_dihedral_types > 0) {
+       fprintf(DatF,"AngleAngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].angleangledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"EndBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ", 
+		   dihedraltypes[i].endbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"MiddleBondTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 4; j++)
+	   fprintf(DatF,"%10.4f ", 
+		   dihedraltypes[i].midbonddihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+
+       fprintf(DatF,"BondBond13 Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 3; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].bond13_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+
+       fprintf(DatF,"AngleTorsion Coeffs\n\n");
+       for (i=0; i < no_dihedral_types; i++) {
+	 fprintf(DatF, "%3i ", i+1);
+	 for ( j = 0; j < 8; j++)
+	   fprintf(DatF, "%10.4f ",
+		   dihedraltypes[i].angledihedral_cross_term[j]);
+	 fprintf(DatF, "\n");
+       }
+       fprintf(DatF, "\n");
+     }
+   }
+
+   /*--------------------------------------------------------------------*/
+
+   /* ATOMS */
+
+   fprintf(DatF, "Atoms\n\n");
+   for(k=0; k < total_no_atoms; k++) {
+     fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f\n",
+              k+1,
+              atoms[k].molecule,                            
+	      atoms[k].type+1,
+              atoms[k].q,
+              atoms[k].x[0],
+	      atoms[k].x[1],
+              atoms[k].x[2]);
+   }
+   fprintf(DatF, "\n");
+
+   /***** BONDS *****/
+
+   if (total_no_bonds > 0) {
+     fprintf(DatF, "Bonds\n\n");
+     for(k=0; k < total_no_bonds; k++)
+       fprintf(DatF, "%6i %3i %6i %6i\n",k+1,
+	       bonds[k].type+1,
+	       bonds[k].members[0]+1,
+	       bonds[k].members[1]+1);
+     fprintf(DatF,"\n");
+   }
+
+   /***** ANGLES *****/
+
+   if (total_no_angles > 0) {
+     fprintf(DatF, "Angles\n\n");
+     for(k=0; k < total_no_angles; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i\n",k+1,
+	       angles[k].type+1,
+	       angles[k].members[0]+1,
+	       angles[k].members[1]+1,
+	       angles[k].members[2]+1);
+     fprintf(DatF, "\n");
+   }
+
+
+   /***** TORSIONS *****/
+
+   if (total_no_dihedrals > 0)   {
+      fprintf(DatF,"Dihedrals\n\n");
+      for(k=0; k < total_no_dihedrals; k++)
+	fprintf(DatF, "%6i %3i %6i %6i %6i %6i\n",k+1,
+		dihedrals[k].type+1,
+		dihedrals[k].members[0]+1,
+		dihedrals[k].members[1]+1,
+		dihedrals[k].members[2]+1,
+		dihedrals[k].members[3]+1);
+      fprintf(DatF, "\n");
+   }
+
+   /***** OUT-OF-PLANES *****/
+
+   if (total_no_oops+total_no_angle_angles > 0) {
+     fprintf(DatF,"Impropers\n\n");
+     for (k=0; k < total_no_oops; k++)
+       fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n", k+1,
+	       oops[k].type+1,
+	       oops[k].members[0]+1,
+	       oops[k].members[1]+1,
+	       oops[k].members[2]+1,
+	       oops[k].members[3]+1);
+     if (forcefield == 2) {
+       for (k=0; k < total_no_angle_angles; k++)
+	 fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n",k+total_no_oops+1,
+		 angleangles[k].type+no_oop_types+1,
+		 angleangles[k].members[0]+1,
+		 angleangles[k].members[1]+1,
+		 angleangles[k].members[2]+1,
+		 angleangles[k].members[3]+1);
+     }
+     fprintf(DatF, "\n");
+   }
+
+/* Close data file */
+
+   if (fclose(DatF) !=0) {
+      fprintf(stderr,"Error closing %s.lammps05\n", rootname);
+      exit(1);
+   }
+
+}
+

tools/msi2lmp/src/msi2lmp.c

@@ -0,0 +1,275 @@
+/*
+*
+*  msi2lmp.exe  V3.6
+*
+*   v3.6 KLA - Changes to output to either lammps 2001 (F90 version) or to 
+*              lammps 2005 (C++ version)
+*
+*   v3.4 JEC - a number of minor changes due to way newline and EOF are generated
+*              on Materials Studio generated .car and .mdf files as well as odd
+*              behavior out of newer Linux IO libraries. ReadMdfFile was restructured
+*              in the process.
+*
+*   v3.1 JEC - changed IO interface to standard in/out, forcefield file
+*              location can be indicated by environmental variable; added 
+*              printing options, consistency checks and forcefield
+*              parameter versions sensitivity (highest one used)
+*
+*   v3.0 JEC - program substantially rewritten to reduce execution time
+*              and be 98 % dynamic in memory use (still fixed limits on
+*              number of parameter types for different internal coordinate
+*              sets)
+*
+*   v2.0 MDP - got internal coordinate information from mdf file and
+*              forcefield parameters from frc file thus eliminating 
+*              need for Discover
+*
+*   V1.0 SL  - original version. Used .car file and internal coordinate
+*              information from Discover to produce LAMMPS data file.
+*
+*  This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
+*  program to produce a LAMMPS data file.
+*
+*  The program is started by supplying information at the command prompt
+* according to the usage described below.  
+*
+*  USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} -2001
+*
+*  -- msi2lmp3 is the name of the executable
+*  -- ROOTNAME is the base name of the .car and .mdf files
+*
+*  -- -print
+*        # is the print level:  0  - silent except for errors
+*                               1  - minimal (default)
+*                               2  - more verbose 
+*  -- -class 
+*        # is the class of forcefield to use (I  = Class I e.g., CVFF)
+*		  			     (II = Class II e.g., CFFx )
+*     default is -class I
+*
+*  -- -frc   - specifies name of the forcefield file (e.g., cff91)
+* 
+*     If the name includes a hard wired directory (i.e., if the name
+*     starts with . or /), then the name is used alone. Otherwise,
+*     the program looks for the forcefield file in $BIOSYM_LIBRARY.
+*     If $BIOSYM_LIBRARY is not set, then the current directory is 
+*     used.
+*
+*     If the file name does not include a dot after the first
+*     character, then .frc is appended to the name.
+*
+*     For example,  -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
+*                              or .)
+*
+*                   -frc cff/cff91 (assumes cff91.frc is in 
+*                                   $BIOSYM_LIBRARY/cff or ./cff)
+*
+*                   -frc /usr/local/biosym/forcefields/cff95 (absolute
+*                                                             location)
+*
+*     By default, the program uses $BIOSYM_LIBRARY/cvff.frc
+*
+*  -- -2001 will output a data file for the FORTRAN 90 version of LAMMPS (2001)
+*     By default, the program will output for the C++ version of LAMMPS.
+*
+*  -- output is written to a file called ROOTNAME.lammps{01/05}
+*
+*
+****************************************************************
+*
+* Msi2lmp3
+*
+* This is the third version of a program that generates a LAMMPS
+* data file based on the information in a MSI car file (atom
+* coordinates) and mdf file (molecular topology). A key part of
+* the program looks up forcefield parameters from an MSI frc file.
+*
+* The first version was written by Steve Lustig at Dupont, but
+* required using Discover to derive internal coordinates and
+* forcefield parameters
+*
+* The second version was written by Michael Peachey while an
+* in intern in the Cray Chemistry Applications Group managed
+* by John Carpenter. This version derived internal coordinates
+* from the mdf file and looked up parameters in the frc file
+* thus eliminating the need for Discover.
+*
+* The third version was written by John Carpenter to optimize
+* the performance of the program for large molecular systems
+* (the original  code for deriving atom numbers was quadratic in time)
+* and to make the program fully dynamic. The second version used
+* fixed dimension arrays for the internal coordinates.
+*
+* John Carpenter can be contacted by sending email to
+* jec374@earthlink.net
+*
+* November 2000
+*/
+
+#define MAIN
+
+#include "Msi2LMP2.h"
+
+int main (int argc, char *argv[])
+{
+   int n,i,found_dot;		/* Counter */
+   int outv;
+   char *string;
+   char *frc_dir_name;
+   char *frc_file_name;
+   FILE *DatF;
+
+ /* Functions called from within main */
+
+/* All code is located in .c file with function name */
+   extern void FrcMenu();
+   extern void ReadCarFile();
+   extern void ReadMdfFile();
+   extern void ReadFrcFile();
+   extern void MakeLists();
+   extern void GetParameters(int);
+   extern void CheckLists();
+   extern void WriteDataFile(FILE *,char *,int);
+
+
+   outv = 2005;
+   pflag = 1;
+   forcefield = 1;		/* Variable that identifies forcefield to use */
+
+   frc_file_name = (char *) calloc(160,sizeof(char));
+   frc_dir_name = (char *) calloc(160,sizeof(char));
+
+   frc_dir_name = getenv("BIOSYM_LIBRARY");
+
+   if (frc_dir_name == NULL) {
+     frc_file_name = strcpy(frc_file_name,"./cvff.frc");
+   }
+   else {
+     for (i=0; i < strlen(frc_dir_name); i++)
+       frc_file_name[i] = frc_dir_name[i];
+     frc_file_name = strcat(frc_file_name,"/cvff.frc");
+   }
+
+   if (argc < 2) { /* If no rootname was supplied, prompt for it */
+     fprintf(stderr,"The rootname of the .car and .mdf files must be entered\n");
+   }
+   else /* rootname was supplied as first argument, copy to rootname */
+     sprintf(rootname,"%s",argv[1]);
+
+   n = 2;
+   while (n < argc) {
+     if (strcmp(argv[n],"-class") == 0) {
+       if (strcmp(argv[n+1],"I") == 0) {
+	 forcefield = 1;
+	 n++;
+       }
+       else if (strcmp(argv[n+1],"II") == 0) {
+	 forcefield = 2;
+	 n++;
+       }
+       else {
+	 fprintf(stderr,"Unrecognized Forcefield class: %s\n",
+		argv[n+1]);
+	 n++;
+       }
+     }
+     else if (strcmp(argv[n],"-2001") == 0) {
+       outv = 2001;
+       n++;
+     }
+     else if (strcmp(argv[n],"-frc") == 0) {
+       if ((frc_dir_name != NULL) && (argv[n+1][0] != '.')) {
+	 for (i=0; i < strlen(frc_dir_name); i++) {
+	   frc_file_name[i] = frc_dir_name[i];
+	 }
+	 frc_file_name[strlen(frc_dir_name)] = '\0';
+	 frc_file_name = strcat(frc_file_name,"/");
+	 frc_file_name = strcat(frc_file_name,argv[n+1]);
+       }
+       else {
+	 frc_file_name = strcpy(frc_file_name,argv[n+1]);
+       }
+       found_dot = 0;
+       for (i=1; i < strlen(frc_file_name); i++) {
+	 if (frc_file_name[i] == '.') found_dot = 1;
+       }
+       if (found_dot == 0) 
+	 frc_file_name = strcat(frc_file_name,".frc");
+       n++;
+     }
+     else if (strstr(argv[n],"-p") != NULL) {
+       pflag = atoi(argv[n+1]);
+       n++;
+     }
+     else {
+       fprintf(stderr,"Unrecognized option: %s\n",argv[n]);
+     }
+     n++;
+   }
+   for (i=0; i < strlen(frc_file_name); i++) 
+     FrcFileName[i] = frc_file_name[i];
+   free(frc_file_name);
+
+   if (pflag > 0) {
+     fprintf(stderr,"\nRunning Msi2lmp.....\n\n");
+     fprintf(stderr," Forcefield file name: %s\n",FrcFileName);
+     fprintf(stderr," Forcefield class: %d\n\n",forcefield);
+   }
+
+   if (((forcefield == 1) && (strstr(FrcFileName,"cff") != NULL) ||
+	(forcefield == 2) && (strstr(FrcFileName,"cvff") != NULL))) {
+     fprintf(stderr," WARNING - forcefield name and class appear to\n");
+     fprintf(stderr,"           be inconsistent - Errors may result\n\n");
+   }
+
+ /* Read in .car file */
+
+   ReadCarFile();
+
+ /*Read in .mdf file */
+
+   ReadMdfFile();
+
+ /* Define bonds, angles, etc...*/
+
+   if (pflag > 0) fprintf(stderr,"\n Building internal coordinate lists \n");
+   MakeLists();
+
+ /* Read .frc file into memory */
+
+   if (pflag > 0) fprintf(stderr,"\n Reading forcefield file \n");
+   ReadFrcFile();
+
+ /* Get forcefield parameters */
+
+   if (pflag > 0) fprintf(stderr,"\n Get parameters for this molecular system\n");
+   GetParameters(forcefield);
+
+  /* Do internal check of internal coordinate lists */
+
+   if (pflag > 0) fprintf(stderr,"\n Check parameters for internal consistency\n");
+   CheckLists();
+
+   if (outv == 2001) {  fprintf(stderr,"\n Writing LAMMPS 2001 data file\n");
+   WriteDataFile01(rootname,forcefield);
+   }
+   else if (outv == 2005) {fprintf(stderr,"\n Writing LAMMPS 2005 data file\n");
+   WriteDataFile05(rootname,forcefield);
+   }
+
+   if (pflag > 0) fprintf(stderr,"\nNormal program termination\n");
+}
+#include <ctype.h>
+int blank_line(char *line)
+{
+  int i,n;
+  for (i=0,n=0; i < strlen(line); i++) {
+    if (isalnum((unsigned char)line[i])) n++;
+  }
+  if (n > 0) {
+    return(0);
+  }
+  else {
+    return(1);
+  }
+}

tools/msi2lmp/test/correct/data.nylon

@@ -0,0 +1,898 @@
+LAMMPS data file for nylon
+
+    117 atoms
+    116 bonds
+    219 angles
+    311 dihedrals
+     11 impropers
+
+   8 atom types
+  10 bond types
+  19 angle types
+  25 dihedral types
+   3 improper types
+
+    -2.085999966    11.720000267 xlo xhi
+     3.098999977    22.469999313 ylo yhi
+    -1.845999956    35.515998840 zlo zhi
+
+Masses
+
+   1  12.011150
+   2  14.006700
+   3  12.011150
+   4  15.999400
+   5   1.007970
+   6   1.007970
+   7  15.999400
+   8  14.006700
+
+Nonbond Coeffs
+
+   1   0.0389999952   3.8754094636 
+   2   0.1669999743   3.5012320066 
+   3   0.1479999981   3.6170487995 
+   4   0.2280000124   2.8597848722 
+   5   0.0380000011   2.4499714540 
+   6   0.0000000000   0.0000000000 
+   7   0.2280000124   2.8597848722 
+   8   0.1669999743   3.5012320066 
+
+Bond Coeffs
+
+  1   322.7158     1.5260 
+  2   340.6175     1.1050 
+  3   356.5988     1.4700 
+  4   377.5752     1.4600 
+  5   388.0000     1.3200 
+  6   483.4512     1.0260 
+  7   615.3220     1.2300 
+  8   283.0924     1.5200 
+  9   540.0000     1.2500 
+ 10   457.4592     1.0260 
+
+Angle Coeffs
+
+  1    44.4000   110.0000 
+  2    50.0000   109.5000 
+  3    39.5000   106.4000 
+  4    57.3000   109.5000 
+  5    46.6000   110.5000 
+  6    50.0000   109.5000 
+  7    51.5000   109.5000 
+  8   111.0000   118.0000 
+  9    35.0000   122.0000 
+ 10    37.5000   115.0000 
+ 11    68.0000   120.0000 
+ 12    53.5000   114.1000 
+ 13    68.0000   120.0000 
+ 14    46.6000   110.5000 
+ 15    45.0000   109.5000 
+ 16    68.0000   120.0000 
+ 17   145.0000   123.0000 
+ 18    41.6000   110.0000 
+ 19    36.0000   105.5000 
+
+Dihedral Coeffs
+
+  1     0.1581     1.0000     3.0000 
+  2     0.1581     1.0000     3.0000 
+  3     0.1581     1.0000     3.0000 
+  4     0.1581     1.0000     3.0000 
+  5     0.0889     1.0000     3.0000 
+  6     0.0889     1.0000     3.0000 
+  7     0.1581     1.0000     3.0000 
+  8     0.1581     1.0000     3.0000 
+  9     0.1581     1.0000     3.0000 
+ 10     0.0000     1.0000     0.0000 
+ 11     0.0000     1.0000     0.0000 
+ 12     0.0000     1.0000     0.0000 
+ 13     0.0000     1.0000     0.0000 
+ 14     3.8000    -1.0000     2.0000 
+ 15     3.2000    -1.0000     2.0000 
+ 16     1.8000    -1.0000     2.0000 
+ 17     1.2000    -1.0000     2.0000 
+ 18     0.0000     1.0000     0.0000 
+ 19     0.0000     1.0000     0.0000 
+ 20     0.0000     1.0000     0.0000 
+ 21     0.0000     1.0000     0.0000 
+ 22     0.1581     1.0000     3.0000 
+ 23     0.1581     1.0000     3.0000 
+ 24     0.0000     1.0000     0.0000 
+ 25     0.0000     1.0000     0.0000 
+
+Improper Coeffs
+
+  1    10.0000    -1.0000     2.0000 
+  2    10.0000    -1.0000     2.0000 
+  3    11.6000    -1.0000     2.0000 
+
+Atoms
+
+      1      0   1  0.220000     1.493000031    20.593999863    -0.449999988
+      2      0   1 -0.200000     2.328000069    19.871000290     0.623000026
+      3      0   1 -0.200000     2.887000084    20.902999878     1.621000051
+      4      0   1 -0.200000     3.533999920    20.169000626     2.809999943
+      5      0   1 -0.200000     4.085000038    21.201000214     3.812999964
+      6      0   1  0.020000     4.731999874    20.466999054     5.001999855
+      7      0   2 -0.500000     5.270999908    21.479000092     5.985000134
+      8      0   3  0.380000     6.477000237    21.142000198     6.829999924
+      9      0   4 -0.380000     7.435999870    22.232000351     7.244999886
+     10      0   1 -0.200000     6.728000164    19.687000275     7.267000198
+     11      0   1 -0.200000     7.763999939    19.665000916     8.406999588
+     12      0   1 -0.200000     7.464000225    18.486000061     9.350999832
+     13      0   1 -0.200000     8.416000366    18.541000366    10.560999870
+     14      0   3  0.380000     8.112999916    17.364999771    11.506999969
+     15      0   4 -0.380000     6.711999893    16.809000015    11.597000122
+     16      0   5  0.100000     2.111000061    20.704999924    -1.401000023
+     17      0   5  0.100000     1.195999980    21.625999451    -0.067000002
+     18      0   5  0.100000     3.191999912    19.319000244     0.125000000
+     19      0   5  0.100000     1.669999957    19.124000549     1.179000020
+     20      0   5  0.100000     3.670000076    21.548999786     1.101999998
+     21      0   5  0.100000     2.039000034    21.563999176     1.998999953
+     22      0   5  0.100000     4.388000011    19.513999939     2.434000015
+     23      0   5  0.100000     2.753999949    19.517999649     3.325999975
+     24      0   5  0.100000     4.866000175    21.853000641     3.298000097
+     25      0   5  0.100000     3.232000113    21.857000351     4.190000057
+     26      0   5  0.100000     5.585000038    19.811000824     4.625999928
+     27      0   5  0.100000     3.951999903    19.815999985     5.518000126
+     28      0   6  0.280000     4.782000065    22.469999313     6.085999966
+     29      0   5  0.100000     7.124000072    19.086999893     6.382999897
+     30      0   5  0.100000     5.751999855    19.225000381     7.632999897
+     31      0   5  0.100000     8.809000015    19.542999268     7.967999935
+     32      0   5  0.100000     7.709000111    20.642000198     8.989999771
+     33      0   5  0.100000     7.614999771    17.503000259     8.793999672
+     34      0   5  0.100000     6.385000229    18.555000305     9.713999748
+     35      0   5  0.100000     9.494999886    18.468999863    10.199000359
+     36      0   5  0.100000     8.267000198    19.524000168    11.118000031
+     37      0   2 -0.500000     9.217000008    16.766000748    12.345000267
+     38      0   1  0.020000     8.902999878    16.179000854    13.701000214
+     39      0   1 -0.200000     9.892000198    15.039999962    14.008999825
+     40      0   1 -0.200000     9.138999939    13.871000290    14.671999931
+     41      0   1 -0.200000    10.074000359    12.652999878    14.779999733
+     42      0   1 -0.200000     9.317999840    11.480999947    15.434000015
+     43      0   1  0.020000    10.253000259    10.262000084    15.543000221
+     44      0   2 -0.500000     9.512000084     9.114000320    16.184000015
+     45      0   3  0.380000    10.263999939     8.095999718    17.007999420
+     46      0   4 -0.380000    11.720000267     8.319999695    17.337999344
+     47      0   1 -0.200000     9.545000076     6.831999779    17.513000488
+     48      0   1 -0.200000    10.385999680     6.170000076    18.621000290
+     49      0   1 -0.200000     9.451999664     5.482999802    19.634000778
+     50      0   1 -0.200000    10.281999588     4.934999943    20.809999466
+     51      0   5  0.100000    10.808575630     5.755126953    21.298067093
+     52      0   5  0.100000    11.006152153     4.209916592    20.438573837
+     53      0   3  0.380000     9.347999573     4.250999928    21.825000763
+     54      0   4 -0.380000     9.854000092     3.098999977    22.659999847
+     55      0   6  0.280000    10.260000229    16.757999420    11.965000153
+     56      0   5  0.100000     8.998000145    16.989000320    14.496999741
+     57      0   5  0.100000     7.839000225    15.769000053    13.699999809
+     58      0   5  0.100000    10.701999664    15.418999672    14.715999603
+     59      0   5  0.100000    10.373000145    14.680000305    13.039999962
+     60      0   5  0.100000     8.796999931    14.180999756    15.713999748
+     61      0   5  0.100000     8.229999542    13.597000122    14.039999962
+     62      0   5  0.100000    10.979000092    12.923000336    15.418000221
+     63      0   5  0.100000    10.421999931    12.345999718    13.739000320
+     64      0   5  0.100000     8.970999718    11.786999702    16.475999832
+     65      0   5  0.100000     8.413000107    11.208999634    14.796999931
+     66      0   5  0.100000    11.159000397    10.532999992    16.180000305
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+   155   2     64     42     43     67
+   156   9     44     43     42     65
+   157   2     65     42     43     66
+   158   2     65     42     43     67
+   159  10     42     43     44     45
+   160  11     42     43     44     68
+   161  12     66     43     44     45
+   162  13     66     43     44     68
+   163  12     67     43     44     45
+   164  13     67     43     44     68
+   165  14     43     44     45     46
+   166  15     43     44     45     47
+   167  16     68     44     45     46
+   168  17     68     44     45     47
+   169  18     48     47     45     44
+   170  19     69     47     45     44
+   171  19     70     47     45     44
+   172  20     48     47     45     46
+   173  21     69     47     45     46
+   174  21     70     47     45     46
+   175  22     49     48     47     45
+   176  23     45     47     48     71
+   177  23     45     47     48     72
+   178   1     49     48     47     69
+   179   2     69     47     48     71
+   180   2     69     47     48     72
+   181   1     49     48     47     70
+   182   2     70     47     48     71
+   183   2     70     47     48     72
+   184   7     47     48     49     50
+   185   1     47     48     49     73
+   186   1     47     48     49     74
+   187   1     50     49     48     71
+   188   2     71     48     49     73
+   189   2     71     48     49     74
+   190   1     50     49     48     72
+   191   2     72     48     49     73
+   192   2     72     48     49     74
+   193  22     48     49     50     53
+   194   1     48     49     50     51
+   195   1     48     49     50     52
+   196  23     53     50     49     73
+   197   2     73     49     50     51
+   198   2     73     49     50     52
+   199  23     53     50     49     74
+   200   2     74     49     50     51
+   201   2     74     49     50     52
+   202  20     49     50     53     54
+   203  18     49     50     53     75
+   204  21     51     50     53     54
+   205  19     51     50     53     75
+   206  21     52     50     53     54
+   207  19     52     50     53     75
+   208  15     76     75     53     50
+   209  17     91     75     53     50
+   210  14     76     75     53     54
+   211  16     91     75     53     54
+   212  10     77     76     75     53
+   213  12     92     76     75     53
+   214  12     93     76     75     53
+   215  11     77     76     75     91
+   216  13     92     76     75     91
+   217  13     93     76     75     91
+   218   8     78     77     76     75
+   219   9     75     76     77     94
+   220   9     75     76     77     95
+   221   1     78     77     76     92
+   222   2     92     76     77     94
+   223   2     92     76     77     95
+   224   1     78     77     76     93
+   225   2     93     76     77     94
+   226   2     93     76     77     95
+   227   7     76     77     78     79
+   228   1     76     77     78     96
+   229   1     76     77     78     97
+   230   1     79     78     77     94
+   231   2     94     77     78     96
+   232   2     94     77     78     97
+   233   1     79     78     77     95
+   234   2     95     77     78     96
+   235   2     95     77     78     97
+   236   7     77     78     79     80
+   237   1     77     78     79     98
+   238   1     77     78     79     99
+   239   1     80     79     78     96
+   240   2     96     78     79     98
+   241   2     96     78     79     99
+   242   1     80     79     78     97
+   243   2     97     78     79     98
+   244   2     97     78     79     99
+   245   7     78     79     80     81
+   246   1     78     79     80    100
+   247   1     78     79     80    101
+   248   1     81     80     79     98
+   249   2     98     79     80    100
+   250   2     98     79     80    101
+   251   1     81     80     79     99
+   252   2     99     79     80    100
+   253   2     99     79     80    101
+   254   8     79     80     81     82
+   255   1     79     80     81    102
+   256   1     79     80     81    103
+   257   9     82     81     80    100
+   258   2    100     80     81    102
+   259   2    100     80     81    103
+   260   9     82     81     80    101
+   261   2    101     80     81    102
+   262   2    101     80     81    103
+   263  10     80     81     82     83
+   264  11     80     81     82    104
+   265  12    102     81     82     83
+   266  13    102     81     82    104
+   267  12    103     81     82     83
+   268  13    103     81     82    104
+   269  14     81     82     83     84
+   270  15     81     82     83     85
+   271  16    104     82     83     84
+   272  17    104     82     83     85
+   273  18     86     85     83     82
+   274  19    105     85     83     82
+   275  19    106     85     83     82
+   276  20     86     85     83     84
+   277  21    105     85     83     84
+   278  21    106     85     83     84
+   279  22     87     86     85     83
+   280  23     83     85     86    107
+   281  23     83     85     86    108
+   282   1     87     86     85    105
+   283   2    105     85     86    107
+   284   2    105     85     86    108
+   285   1     87     86     85    106
+   286   2    106     85     86    107
+   287   2    106     85     86    108
+   288   7     85     86     87     88
+   289   1     85     86     87    109
+   290   1     85     86     87    110
+   291   1     88     87     86    107
+   292   2    107     86     87    109
+   293   2    107     86     87    110
+   294   1     88     87     86    108
+   295   2    108     86     87    109
+   296   2    108     86     87    110
+   297  22     86     87     88     89
+   298   1     86     87     88    111
+   299   1     86     87     88    112
+   300  23     89     88     87    109
+   301   2    109     87     88    111
+   302   2    109     87     88    112
+   303  23     89     88     87    110
+   304   2    110     87     88    111
+   305   2    110     87     88    112
+   306  24     87     88     89     90
+   307  24     87     88     89    113
+   308  25    111     88     89     90
+   309  25    111     88     89    113
+   310  25    112     88     89     90
+   311  25    112     88     89    113
+
+Impropers
+
+     1   1     28      7      6      8 
+     2   2     10      8      7      9 
+     3   2     13     14     37     15 
+     4   1     55     37     38     14 
+     5   1     68     44     43     45 
+     6   2     47     45     44     46 
+     7   2     50     53     75     54 
+     8   1     91     75     76     53 
+     9   1    104     82     81     83 
+    10   2     85     83     82     84 
+    11   3     88     89     90    113 
+

tools/msi2lmp/test/correct/data.phen3_cff97

@@ -0,0 +1,442 @@
+LAMMPS data file for phen3_cff97
+
+     23 atoms
+     23 bonds
+     39 angles
+     54 dihedrals
+     19 impropers
+
+   7 atom types
+   9 bond types
+  16 angle types
+  19 dihedral types
+  12 improper types
+
+    -0.483345032     3.619415522 xlo xhi
+    -5.980008125     2.346019268 ylo yhi
+    -2.715474367     0.916701555 zlo zhi
+
+Masses
+
+   1  14.006700
+   2   1.007970
+   3  12.011150
+   4   1.007970
+   5  12.011150
+   6  15.999400
+   7  12.011150
+
+Nonbond Coeffs
+
+   1   0.0650000000   3.2620000000 
+   2   0.0130000000   1.0980000000 
+   3   0.0540000000   4.0100000000 
+   4   0.0200000000   2.9950000000 
+   5   0.1200000000   3.9080000000 
+   6   0.1670000000   3.5960000000 
+   7   0.0640000000   4.0100000000 
+
+Bond Coeffs
+
+  1     1.5185   293.1700  -603.7882   629.6900 
+  2     1.0119   448.6300  -963.1917  1248.4000 
+  3     1.1010   341.0000  -691.8900   844.6000 
+  4     1.5483   253.0800  -449.0300   457.3200 
+  5     1.5330   299.6700  -501.7700   679.8100 
+  6     1.2339   711.3500 -1543.9000  1858.6000 
+  7     1.5010   321.9021  -521.8208   572.1628 
+  8     1.4314   356.0904  -627.6179  1327.6345 
+  9     1.0862   377.7644  -803.4526   894.3173 
+
+Angle Coeffs
+
+  1   110.5100    49.2170   -12.2153   -18.9667 
+  2   106.1100    45.3280   -14.0474     1.9350 
+  3   105.8500    72.2630   -28.1923     0.0000 
+  4     0.0000     0.0000     0.0000     0.0000 
+  5   112.1300    66.4520     4.8694    37.7860 
+  6   109.6700    37.9190    -7.3877    -8.0694 
+  7   110.7700    41.4530   -10.6040     5.1290 
+  8   104.4900    31.3750    -4.4023    -6.5271 
+  9   115.0600    59.0960   -15.1430   -12.9820 
+ 10   130.0100   111.2900   -52.3390   -28.1070 
+ 11   108.4000    43.9594    -8.3924    -9.3379 
+ 12   107.6600    39.6410   -12.9210    -2.4318 
+ 13   111.0000    44.3234    -9.4454     0.0000 
+ 14   120.0500    44.7148   -22.7352     0.0000 
+ 15   118.9000    61.0226   -34.9931     0.0000 
+ 16   117.9400    35.1558   -12.4682     0.0000 
+
+Dihedral Coeffs
+
+  1    -0.2458     0.0000    -0.2789     0.0000    -0.0294     0.0000 
+  2     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000 
+  3    -0.8792     0.0000    -0.5978     0.0000    -0.3242     0.0000 
+  4     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000 
+  5    -2.5999     0.0000     1.0488     0.0000    -0.2089     0.0000 
+  6     1.7311     0.0000     1.8510     0.0000    -0.1933     0.0000 
+  7    -0.2179     0.0000    -0.4127     0.0000    -0.1252     0.0000 
+  8     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000 
+  9    -0.2432     0.0000     0.0617     0.0000    -0.1383     0.0000 
+ 10    -0.0228     0.0000     0.0280     0.0000    -0.1863     0.0000 
+ 11    -1.2767     0.0000     0.5949     0.0000     0.2379     0.0000 
+ 12     0.0972     0.0000     0.0722     0.0000    -0.2581     0.0000 
+ 13    -0.2802     0.0000    -0.0678     0.0000    -0.0122     0.0000 
+ 14    -0.2802     0.0000    -0.0678     0.0000    -0.0122     0.0000 
+ 15     0.0000     0.0000     1.5590     0.0000     0.0000     0.0000 
+ 16     0.0000     0.0000     4.4072     0.0000     0.0000     0.0000 
+ 17     0.0000     0.0000     3.9661     0.0000     0.0000     0.0000 
+ 18     8.3667     0.0000     1.1932     0.0000     0.0000     0.0000 
+ 19     0.0000     0.0000     1.8769     0.0000     0.0000     0.0000 
+
+Improper Coeffs
+
+  1    44.1500     0.0000 
+  2     6.9644     0.0000 
+  3     7.6012     0.0000 
+  4     0.0000     0.0000 
+  5     0.0000     0.0000 
+  6     0.0000     0.0000 
+  7     0.0000     0.0000 
+  8     0.0000     0.0000 
+  9     0.0000     0.0000 
+ 10     0.0000     0.0000 
+ 11     0.0000     0.0000 
+ 12     0.0000     0.0000 
+
+BondBond Coeffs
+
+  1     8.6951     1.0119     1.5185 
+  2     2.8266     1.0119     1.0119 
+  3    -1.4797     1.5185     1.1010 
+  4     0.0000     1.5185     1.5483 
+  5    16.4280     1.5185     1.5330 
+  6    -1.1701     1.1010     1.5483 
+  7     3.3872     1.5330     1.1010 
+  8    16.4650     1.5330     1.5483 
+  9    57.8750     1.5483     1.2339 
+ 10   166.5900     1.2339     1.2339 
+ 11     0.0000     1.5330     1.5010 
+ 12     5.3316     1.1010     1.1010 
+ 13     2.9168     1.1010     1.5010 
+ 14    12.0676     1.5010     1.4314 
+ 15    68.2856     1.4314     1.4314 
+ 16     1.0795     1.0862     1.4314 
+
+BondAngle Coeffs
+
+  1     6.2182    27.8810     1.0119     1.5185 
+  2    10.1080    10.1080     1.0119     1.0119 
+  3    50.0180    15.8820     1.5185     1.1010 
+  4     0.0000     0.0000     1.5185     1.5483 
+  5    49.7730    14.0620     1.5185     1.5330 
+  6    14.9650    11.8650     1.1010     1.5483 
+  7    20.7540    11.4210     1.5330     1.1010 
+  8    23.0840    19.1590     1.5330     1.5483 
+  9    51.5840    62.0560     1.5483     1.2339 
+ 10    73.3500    73.3500     1.2339     1.2339 
+ 11     0.0000     0.0000     1.5330     1.5010 
+ 12    18.1030    18.1030     1.1010     1.1010 
+ 13    11.7717    26.4608     1.1010     1.5010 
+ 14    47.0579    31.0771     1.5010     1.4314 
+ 15    28.8708    28.8708     1.4314     1.4314 
+ 16    24.2183    20.0033     1.0862     1.4314 
+
+AngleAngle Coeffs
+
+  1     0.0000     0.0000     0.0000   115.0600   130.0100   115.0600 
+  2     0.0000     0.0000     0.0000   120.0500   118.9000   120.0500 
+  3     0.0000     0.0000     0.0000   117.9400   118.9000   117.9400 
+  4    -2.0310    -2.0310    -3.6257   106.1100   110.5100   110.5100 
+  5    -1.9852    -1.9852    -1.9852   106.1100   106.1100   106.1100 
+  6     0.0000     0.0000     0.0000   105.8500   109.6700     0.0000 
+  7     6.0274     7.0292     4.2440   112.1300   110.7700   105.8500 
+  8     0.0000     0.0000     0.0000   112.1300   104.4900     0.0000 
+  9     2.4594    -1.0033    -0.0414   110.7700   109.6700   104.4900 
+ 10     0.2738    -0.4825     0.2738   110.7700   107.6600   110.7700 
+ 11     1.0827    -1.8202     2.0403   110.7700   111.0000   108.4000 
+ 12     2.3794     2.3794     3.0118   107.6600   111.0000   111.0000 
+
+AngleAngleTorsion Coeffs
+
+  1    -9.0674   110.5100   105.8500 
+  2     0.0000   110.5100     0.0000 
+  3   -15.9511   110.5100   112.1300 
+  4     0.0000     0.0000   115.0600 
+  5   -19.4570   109.6700   115.0600 
+  6   -28.7420   104.4900   115.0600 
+  7   -18.9263   112.1300   110.7700 
+  8     0.0000   112.1300   108.4000 
+  9   -12.5640   110.7700   110.7700 
+ 10     0.0000   110.7700   108.4000 
+ 11   -15.6070   110.7700   104.4900 
+ 12     0.0000   104.4900   108.4000 
+ 13     0.0000   108.4000   120.0500 
+ 14    -5.8888   111.0000   120.0500 
+ 15     4.4444   120.0500   117.9400 
+ 16   -14.4097   120.0500   118.9000 
+ 17    -4.8141   117.9400   118.9000 
+ 18     0.0000   118.9000   118.9000 
+ 19     0.3598   117.9400   117.9400 
+
+EndBondTorsion Coeffs
+
+1     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.0119     1.1010 
+2     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.0119     1.5483 
+3     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.0119     1.5330 
+4     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5185     1.2339 
+5     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.1010     1.2339 
+6     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5330     1.2339 
+7     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5185     1.1010 
+8     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5185     1.5010 
+9     0.2130     0.3120     0.0777     0.2130     0.3120     0.0777     1.1010     1.1010 
+10     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.1010     1.5010 
+11     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.1010     1.5483 
+12     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5483     1.5010 
+13     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     1.5330     1.4314 
+14     1.3997     0.7756     0.0000    -0.5835     1.1220     0.3978     1.1010     1.4314 
+15     0.0000    -1.7970     0.0000     0.0000    -0.4879     0.0000     1.5010     1.0862 
+16     0.0000     0.2421     0.0000     0.0000    -0.6918     0.0000     1.5010     1.4314 
+17     0.0000    -0.4669     0.0000     0.0000    -6.8958     0.0000     1.0862     1.4314 
+18    -0.1185     6.3204     0.0000    -0.1185     6.3204     0.0000     1.4314     1.4314 
+19     0.0000    -0.6890     0.0000     0.0000    -0.6890     0.0000     1.0862     1.0862 
+
+MiddleBondTorsion Coeffs
+
+  1    -0.6980     0.8910    -0.1895     1.5185 
+  2     0.0000     0.0000     0.0000     1.5185 
+  3    -0.5922    -1.2262     0.4264     1.5185 
+  4     0.0000     0.0000     0.0000     1.5483 
+  5    -5.7009     0.7758    -0.4090     1.5483 
+  6     0.6798     0.9388    -1.8478     1.5483 
+  7    -9.8826    -3.7138    -0.1022     1.5330 
+  8     0.0000     0.0000     0.0000     1.5330 
+  9   -14.2610    -0.5322    -0.4864     1.5330 
+ 10     0.0000     0.0000     0.0000     1.5330 
+ 11   -13.6420    -0.8843     0.2118     1.5330 
+ 12     0.0000     0.0000     0.0000     1.5330 
+ 13     0.0000     0.0000     0.0000     1.5010 
+ 14    -5.5679     1.4083     0.3010     1.5010 
+ 15     0.0000     3.9421     0.0000     1.4314 
+ 16     0.0000     9.1792     0.0000     1.4314 
+ 17     0.0000    -1.1521     0.0000     1.4314 
+ 18    27.5989    -2.3120     0.0000     1.4314 
+ 19     0.0000     4.8228     0.0000     1.4314 
+
+BondBond13 Coeffs
+
+  1     0.0000     1.0119     1.1010 
+  2     0.0000     1.0119     1.5483 
+  3     0.0000     1.0119     1.5330 
+  4     0.0000     1.5185     1.2339 
+  5     0.0000     1.1010     1.2339 
+  6     0.0000     1.5330     1.2339 
+  7     0.0000     1.5185     1.1010 
+  8     0.0000     1.5185     1.5010 
+  9     0.0000     1.1010     1.1010 
+ 10     0.0000     1.1010     1.5010 
+ 11     0.0000     1.1010     1.5483 
+ 12     0.0000     1.5483     1.5010 
+ 13     0.0000     1.5330     1.4314 
+ 14    -3.4826     1.1010     1.4314 
+ 15     0.8743     1.5010     1.0862 
+ 16     2.5085     1.5010     1.4314 
+ 17    -6.2741     1.0862     1.4314 
+ 18   -73.6169     1.4314     1.4314 
+ 19    -1.7077     1.0862     1.0862 
+
+AngleTorsion Coeffs
+
+  1    -1.7705    -0.8407    -0.2881    -2.4112    -0.4658    -0.0738   110.5100   105.8500 
+  2     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   110.5100     0.0000 
+  3    -2.1025    -0.9363     0.4381    -3.5237    -0.3880    -0.4954   110.5100   112.1300 
+  4     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   115.0600 
+  5    12.0720     0.2388    -0.0426    -4.2825     1.1254    -0.1481   109.6700   115.0600 
+  6    13.2220     1.3271    -0.3941     2.9333     2.2593    -0.5573   104.4900   115.0600 
+  7    -2.8694     1.6172    -1.4627    -3.4109     0.6476    -0.9584   112.1300   110.7700 
+  8     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   112.1300   108.4000 
+  9    -0.8085     0.5569    -0.2466    -0.8085     0.5569    -0.2466   110.7700   110.7700 
+ 10     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   110.7700   108.4000 
+ 11     3.9318     2.2235     0.3670     1.6575    -0.4577     0.3610   110.7700   104.4900 
+ 12     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   104.4900   108.4000 
+ 13     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000   108.4000   120.0500 
+ 14     4.6266     0.1632     0.0461     0.2251     0.6548     0.1237   111.0000   120.0500 
+ 15     0.0000    -0.1242     0.0000     0.0000     3.4601     0.0000   120.0500   117.9400 
+ 16     0.0000    -4.4683     0.0000     0.0000     3.8987     0.0000   120.0500   118.9000 
+ 17     0.0000     2.7147     0.0000     0.0000     2.5014     0.0000   117.9400   118.9000 
+ 18     1.9767     1.0239     0.0000     1.9767     1.0239     0.0000   118.9000   118.9000 
+ 19     0.0000     2.4501     0.0000     0.0000     2.4501     0.0000   117.9400   117.9400 
+
+Atoms
+
+      1      0   1 -0.045000     0.109592088    -0.199880913     0.000000478
+      2      0   2  0.280000    -0.124733858    -1.202872038    -0.000001981
+      3      0   2  0.280000    -0.285811990     0.244572327     0.840843439
+      4      0   2  0.280000    -0.285812497     0.244576558    -0.840839982
+      5      0   3 -0.078000     1.560634732    -0.038402185     0.000000465
+      6      0   4  0.053000     1.972637177    -0.500293911     0.916701555
+      7      0   5  0.297400     1.942531705     1.422506809     0.000000450
+      8      0   6 -0.533700     3.187694550     1.672445178     0.000000438
+      9      0   6 -0.533700     1.070737839     2.346019268     0.000000449
+     10      0   3 -0.106000     2.174581766    -0.718786478    -1.261021852
+     11      0   4  0.053000     1.839982390    -0.182426706    -2.172762394
+     12      0   4  0.053000     3.272250891    -0.569177628    -1.261509657
+     13      0   7  0.000000     1.889680982    -2.218492746    -1.435816169
+     14      0   7 -0.130530     0.737977445    -2.629161119    -2.116767168
+     15      0   4  0.130530     0.061427273    -1.894254208    -2.533302307
+     16      0   7 -0.130530     0.424228579    -3.980331659    -2.214080095
+     17      0   4  0.130530    -0.483345032    -4.285143852    -2.715474367
+     18      0   7 -0.130530     1.268485427    -4.931880474    -1.646431088
+     19      0   4  0.130530     1.020345688    -5.980008125    -1.718327641
+     20      0   7 -0.130530     2.423752546    -4.531005859    -0.977356374
+     21      0   4  0.130530     3.074717045    -5.268786907    -0.531340718
+     22      0   7 -0.130530     2.733307123    -3.177516222    -0.869901538
+     23      0   4  0.130530     3.619415522    -2.873045444    -0.331384182
+
+Bonds
+
+     1   1      1      5
+     2   2      1      2
+     3   2      1      3
+     4   2      1      4
+     5   3      5      6
+     6   4      5      7
+     7   5      5     10
+     8   6      7      9
+     9   6      7      8
+    10   3     10     11
+    11   3     10     12
+    12   7     10     13
+    13   8     13     14
+    14   8     13     22
+    15   9     15     14
+    16   8     14     16
+    17   9     17     16
+    18   8     16     18
+    19   9     19     18
+    20   8     18     20
+    21   9     21     20
+    22   8     20     22
+    23   9     23     22
+
+Angles
+
+     1   1      2      1      5
+     2   1      3      1      5
+     3   1      4      1      5
+     4   2      2      1      3
+     5   2      2      1      4
+     6   2      3      1      4
+     7   3      1      5      6
+     8   4      1      5      7
+     9   5      1      5     10
+    10   6      6      5      7
+    11   7     10      5      6
+    12   8     10      5      7
+    13   9      5      7      9
+    14   9      5      7      8
+    15  10      9      7      8
+    16   7      5     10     11
+    17   7      5     10     12
+    18  11      5     10     13
+    19  12     11     10     12
+    20  13     11     10     13
+    21  13     12     10     13
+    22  14     10     13     14
+    23  14     10     13     22
+    24  15     14     13     22
+    25  16     15     14     13
+    26  15     13     14     16
+    27  16     15     14     16
+    28  16     17     16     14
+    29  15     14     16     18
+    30  16     17     16     18
+    31  16     19     18     16
+    32  15     16     18     20
+    33  16     19     18     20
+    34  16     21     20     18
+    35  15     18     20     22
+    36  16     21     20     22
+    37  16     23     22     20
+    38  15     20     22     13
+    39  16     23     22     13
+
+Dihedrals
+
+     1   1      2      1      5      6
+     2   2      2      1      5      7
+     3   3      2      1      5     10
+     4   1      3      1      5      6
+     5   2      3      1      5      7
+     6   3      3      1      5     10
+     7   1      4      1      5      6
+     8   2      4      1      5      7
+     9   3      4      1      5     10
+    10   4      1      5      7      9
+    11   4      1      5      7      8
+    12   5      6      5      7      9
+    13   5      6      5      7      8
+    14   6     10      5      7      9
+    15   6     10      5      7      8
+    16   7      1      5     10     11
+    17   7      1      5     10     12
+    18   8      1      5     10     13
+    19   9      6      5     10     11
+    20   9      6      5     10     12
+    21  10      6      5     10     13
+    22  11     11     10      5      7
+    23  11     12     10      5      7
+    24  12      7      5     10     13
+    25  13      5     10     13     14
+    26  13      5     10     13     22
+    27  14     11     10     13     14
+    28  14     11     10     13     22
+    29  14     12     10     13     14
+    30  14     12     10     13     22
+    31  15     10     13     14     15
+    32  16     10     13     14     16
+    33  17     15     14     13     22
+    34  18     22     13     14     16
+    35  16     10     13     22     20
+    36  15     10     13     22     23
+    37  18     14     13     22     20
+    38  17     23     22     13     14
+    39  17     17     16     14     13
+    40  18     13     14     16     18
+    41  19     15     14     16     17
+    42  17     15     14     16     18
+    43  17     19     18     16     14
+    44  18     14     16     18     20
+    45  19     17     16     18     19
+    46  17     17     16     18     20
+    47  17     21     20     18     16
+    48  18     16     18     20     22
+    49  19     19     18     20     21
+    50  17     19     18     20     22
+    51  17     23     22     20     18
+    52  18     18     20     22     13
+    53  19     21     20     22     23
+    54  17     21     20     22     13
+
+Impropers
+
+     1   1      5      7      9      8 
+     2   2     10     13     14     22 
+     3   3     15     14     13     16 
+     4   3     17     16     14     18 
+     5   3     19     18     16     20 
+     6   3     21     20     18     22 
+     7   3     23     22     20     13 
+     8   4      2      1      3      5 
+     9   4      2      1      4      5 
+    10   4      3      1      4      5 
+    11   5      2      1      3      4 
+    12   6      1      5      6      7 
+    13   7      1      5     10      6 
+    14   8      1      5     10      7 
+    15   9     10      5      6      7 
+    16  10      5     10     11     12 
+    17  11      5     10     11     13 
+    18  11      5     10     12     13 
+    19  12     11     10     12     13 
+

tools/msi2lmp/test/crambin.car

@@ -0,0 +1,649 @@
+!BIOSYM archive 3                                                               
+PBC=OFF                                                                         
+input file for discover                                                         
+!DATE Mon Jul 14 13:41:23 1997                                                  
+N       17.047000885   14.098999977    3.625000000 THRN 1      n4      N  -0.500
+HN3     16.238992691   14.681707382    3.886676073 THRN 1      hn      H   0.360
+HN1     17.917675018   14.581335068    3.889913321 THRN 1      hn      H   0.360
+HN2     17.039421082   13.939416885    2.607465982 THRN 1      hn      H   0.360
+CA      16.966999054   12.784000397    4.337999821 THRN 1      ca      C   0.320
+HA      16.972635269   11.928232193    3.662923098 THRN 1      h       H   0.100
+C       15.685000420   12.755000114    5.132999897 THRN 1      c'      C   0.380
+O       15.267999649   13.824999809    5.593999863 THRN 1      o'      O  -0.380
+CB      18.170000076   12.703000069    5.336999893 THRN 1      c1      C  -0.070
+HB      18.120826721   13.621001244    5.922624588 THRN 1      h       H   0.100
+OG1     19.333999634   12.829000473    4.462999821 THRN 1      oh      O  -0.380
+HG1     19.691650391   13.794054985    4.503693104 THRN 1      ho      H   0.350
+CG2     18.149999619   11.545999527    6.303999901 THRN 1      c3      C  -0.300
+HG21    19.007284164   11.616475105    6.973474979 THRN 1      h       H   0.100
+HG22    17.230155945   11.575787544    6.888035774 THRN 1      h       H   0.100
+HG23    18.198083878   10.608263016    5.750428200 THRN 1      h       H   0.100
+N       15.114999771   11.555000305    5.264999866 THR  2      n       N  -0.500
+HN      15.528337479   10.717791557    4.830105782 THR  2      hn      H   0.280
+CA      13.855999947   11.468999863    6.065999985 THR  2      ca      C   0.120
+HA      13.508913994   12.491562843    6.214313030 THR  2      h       H   0.100
+C       14.163999557   10.784999847    7.379000187 THR  2      c'      C   0.380
+O       14.993000031    9.862000465    7.442999840 THR  2      o'      O  -0.380
+CB      12.732000351   10.711000443    5.261000156 THR  2      c1      C  -0.070
+HB      11.753349304   10.621357918    5.732493877 THR  2      h       H   0.100
+OG1     13.307999611    9.439000130    4.926000118 THR  2      oh      O  -0.380
+HG1     12.585855484    8.833214760    4.510751247 THR  2      ho      H   0.350
+CG2     12.484000206   11.442000389    3.894999981 THR  2      c3      C  -0.300
+HG21    11.803796768   10.849267006    3.283370495 THR  2      h       H   0.100
+HG22    12.044157028   12.421771049    4.081242085 THR  2      h       H   0.100
+HG23    13.431519508   11.563512802    3.370076180 THR  2      h       H   0.100
+N       13.487999916   11.241000175    8.416999817 CYS  3      n       N  -0.500
+HN      12.810626030   12.002311707    8.267102242 CYS  3      hn      H   0.280
+CA      13.659999847   10.706999779    9.786999702 CYS  3      ca      C   0.120
+HA      14.238283157    9.783084869    9.778588295 CYS  3      h       H   0.100
+C       12.269000053   10.430999756   10.322999954 CYS  3      c'      C   0.380
+O       11.392999649   11.307999611   10.185000420 CYS  3      o'      O  -0.380
+CB      14.368000031   11.748000145   10.690999985 CYS  3      c2      C  -0.300
+HB1     13.670405388   12.570071220   10.851186752 CYS  3      h       H   0.100
+HB2     14.606354713   11.254445076   11.633172989 CYS  3      h       H   0.100
+SG      15.885000229   12.425999641   10.015999794 CYS  3      s1      S   0.100
+N       12.019000053    9.272000313   10.928000450 CYS  4      n       N  -0.500
+HN      12.770128250    8.579818726   11.060630798 CYS  4      hn      H   0.280
+CA      10.645999908    8.991000175   11.407999992 CYS  4      ca      C   0.120
+HA      10.045209885    9.855814934   11.126492500 CYS  4      h       H   0.100
+C       10.654000282    8.793000221   12.918999672 CYS  4      c'      C   0.380
+O       11.659000397    8.295999527   13.491000175 CYS  4      o'      O  -0.380
+CB      10.057000160    7.751999855   10.682000160 CYS  4      c2      C  -0.300
+HB1     10.731808662    6.925758839   10.905740738 CYS  4      h       H   0.100
+HB2      9.122684479    7.521792412   11.194015503 CYS  4      h       H   0.100
+SG       9.836999893    8.017999649    8.904000282 CYS  4      s1      S   0.100
+N        9.560999870    9.107999802   13.562999725 PRO  5      n       N  -0.420
+CA       9.447999954    9.034000397   15.012000084 PRO  5      ca      C   0.060
+HA      10.341467857    9.534400940   15.385380745 PRO  5      h       H   0.100
+CD       8.366000175    9.803999901   12.958000183 PRO  5      c2      C   0.060
+HD1      8.002507210    9.270477295   12.079748154 PRO  5      h       H   0.100
+HD2      8.616027832   10.819077492   12.649448395 PRO  5      h       H   0.100
+C        9.288000107    7.670000076   15.605999947 PRO  5      c'      C   0.380
+O        9.489999771    7.519000053   16.819000244 PRO  5      o'      O  -0.380
+CB       8.229999542    9.956999779   15.345000267 PRO  5      c2      C  -0.200
+HB1      7.714309216    9.644173622   16.252912521 PRO  5      h       H   0.100
+HB2      8.527364731   10.997467041   15.475772858 PRO  5      h       H   0.100
+CG       7.337999821    9.786000252   14.114000320 PRO  5      c2      C  -0.200
+HG1      6.782078266    8.848659515   14.135046959 PRO  5      h       H   0.100
+HG2      6.614880562   10.595389366   14.013560295 PRO  5      h       H   0.100
+N        8.875000000    6.685999870   14.795999527 SER  6      n       N  -0.500
+HN       8.693690300    6.898229599   13.804543495 SER  6      hn      H   0.280
+CA       8.673000336    5.314000130   15.279000282 SER  6      ca      C   0.120
+HA       9.487320900    5.098019123   15.970617294 SER  6      h       H   0.100
+C        8.753000259    4.375999928   14.083000183 SER  6      c'      C   0.380
+O        8.725999832    4.857999802   12.923000336 SER  6      o'      O  -0.380
+CB       7.340000153    5.120999813   15.996000290 SER  6      c2      C  -0.170
+HB1      7.303732872    4.135610104   16.460533142 SER  6      h       H   0.100
+HB2      7.204785347    5.896010399   16.750438690 SER  6      h       H   0.100
+OG       6.274000168    5.219999790   15.031000137 SER  6      oh      O  -0.380
+HG       6.086399078    6.211903572   14.826469421 SER  6      ho      H   0.350
+N        8.880999565    3.075000048   14.357999802 ILE  7      n       N  -0.500
+HN       8.958233833    2.761164188   15.335978508 ILE  7      hn      H   0.280
+CA       8.911999702    2.082999945   13.258000374 ILE  7      ca      C   0.120
+HA       9.752125740    2.304961205   12.599957466 ILE  7      h       H   0.100
+C        7.580999851    2.089999914   12.505999565 ILE  7      c'      C   0.380
+O        7.670000076    2.030999899   11.244999886 ILE  7      o'      O  -0.380
+CB       9.206999779    0.676999986   13.923999786 ILE  7      c1      C  -0.100
+HB       8.631069183    0.572530746   14.843504906 ILE  7      h       H   0.100
+CG1     10.713999748    0.702000022   14.312000275 ILE  7      c2      C  -0.200
+HG11    11.291265488    0.728613675   13.387794495 ILE  7      h       H   0.100
+HG12    10.887344360    1.603095889   14.900283813 ILE  7      h       H   0.100
+CG2      8.810999870   -0.476999998   12.968999863 ILE  7      c3      C  -0.300
+HG21     9.032923698   -1.433422685   13.442394257 ILE  7      h       H   0.100
+HG22     7.744652271   -0.418968171   12.750744820 ILE  7      h       H   0.100
+HG23     9.376438141   -0.391609550   12.041049957 ILE  7      h       H   0.100
+CD1     11.185000420   -0.515999973   15.142000198 ILE  7      c3      C  -0.300
+HD11    11.020709038   -1.430322766   14.571805000 ILE  7      h       H   0.100
+HD12    12.246717453   -0.414458960   15.366830826 ILE  7      h       H   0.100
+HD13    10.619837761   -0.562440276   16.072879791 ILE  7      h       H   0.100
+N        6.458000183    2.161999941   13.159000397 VAL  8      n       N  -0.500
+HN       6.476118088    2.187154531   14.188533783 VAL  8      hn      H   0.280
+CA       5.144999981    2.209000111   12.453000069 VAL  8      ca      C   0.120
+HA       5.026936531    1.265246391   11.920561790 VAL  8      h       H   0.100
+C        5.114999771    3.378999949   11.461000443 VAL  8      c'      C   0.380
+O        4.664000034    3.267999887   10.343000412 VAL  8      o'      O  -0.380
+CB       3.994999886    2.354000092   13.477999687 VAL  8      c1      C  -0.100
+HB       4.418568611    3.051678419   14.200449944 VAL  8      h       H   0.100
+CG1      2.716000080    2.891000032   12.869000435 VAL  8      c3      C  -0.300
+HG11     1.981043458    3.059607983   13.656088829 VAL  8      h       H   0.100
+HG12     2.923026085    3.831490993   12.358395576 VAL  8      h       H   0.100
+HG13     2.322393417    2.168816090   12.153719902 VAL  8      h       H   0.100
+CG2      3.757999897    1.031999946   14.208000183 VAL  8      c3      C  -0.300
+HG21     3.374393702    0.292122275   13.505486488 VAL  8      h       H   0.100
+HG22     4.697329521    0.676970363   14.631930351 VAL  8      h       H   0.100
+HG23     3.033046246    1.182916164   15.007855415 VAL  8      h       H   0.100
+N        5.605999947    4.546000004   11.940999985 ALA  9      n       N  -0.500
+HN       5.984637260    4.591287613   12.897809029 ALA  9      hn      H   0.280
+CA       5.598000050    5.767000198   11.081999779 ALA  9      ca      C   0.120
+HA       4.565777779    5.921326160   10.767674446 ALA  9      h       H   0.100
+C        6.440999985    5.526999950    9.850000381 ALA  9      c'      C   0.380
+O        6.052000046    5.933000088    8.744000435 ALA  9      o'      O  -0.380
+CB       6.021999836    6.977000237   11.890999794 ALA  9      c3      C  -0.300
+HB1      5.950239658    7.871601582   11.272420883 ALA  9      h       H   0.100
+HB2      5.369528770    7.081964016   12.757813454 ALA  9      h       H   0.100
+HB3      7.051515102    6.848640919   12.225253105 ALA  9      h       H   0.100
+N        7.646999836    4.908999920   10.005000114 ARG  10     n       N  -0.500
+HN       7.968383789    4.648912430   10.948380470 ARG  10     hn      H   0.280
+CA       8.496000290    4.609000206    8.836999893 ARG  10     ca      C   0.120
+HA       8.672454834    5.551135063    8.318015099 ARG  10     h       H   0.100
+C        7.797999859    3.608999968    7.875999928 ARG  10     c'      C   0.380
+O        7.877999783    3.778000116    6.651000023 ARG  10     o'      O  -0.380
+CB       9.847000122    4.019999981    9.305000305 ARG  10     c2      C  -0.200
+HB1     10.292553902    4.780714035    9.946011543 ARG  10     h       H   0.110
+HB2      9.592742920    3.191395044    9.965959549 ARG  10     h       H   0.110
+CG      10.751999855    3.607000113    8.149000168 ARG  10     c2      C  -0.200
+HG1     11.631093979    3.136696339    8.589575768 ARG  10     h       H   0.130
+HG2     10.187005997    2.897431850    7.544521332 ARG  10     h       H   0.130
+CD      11.225999832    4.698999882    7.243999958 ARG  10     c2      C  -0.160
+HD1     11.795847893    4.300052166    6.404825211 ARG  10     h       H   0.130
+HD2     10.397437096    5.319350719    6.902313709 ARG  10     h       H   0.130
+NE      12.142999649    5.571000099    8.034999847 ARG  10     n       N  -0.560
+CZ      12.758000374    6.609000206    7.442999840 ARG  10     cr      C   0.380
+NH1     12.538999557    6.932000160    6.157999992 ARG  10     n2      N  -0.560
+HH11    11.887275696    6.371951103    5.590105534 ARG  10     hn      H   0.280
+HH12    13.022671700    7.739827156    5.740416050 ARG  10     hn      H   0.280
+NH2     13.600999832    7.322000027    8.201999664 ARG  10     n2      N  -0.560
+HH21    13.756224632    7.059009075    9.185687065 ARG  10     hn      H   0.280
+HH22    14.093895912    8.133021355    7.801752567 ARG  10     hn      H   0.280
+N        7.185999870    2.582000017    8.444999695 SER  11     n       N  -0.500
+HN       7.181996822    2.472300768    9.469133377 SER  11     hn      H   0.280
+CA       6.500000000    1.583999991    7.565000057 SER  11     ca      C   0.120
+HA       7.232992172    1.158654571    6.879504681 SER  11     h       H   0.100
+C        5.381999969    2.312999964    6.772999763 SER  11     c'      C   0.380
+O        5.212999821    2.016000032    5.557000160 SER  11     o'      O  -0.380
+CB       5.907999992    0.462000012    8.399999619 SER  11     c2      C  -0.170
+HB1      5.275885105    0.867496729    9.190001488 SER  11     h       H   0.100
+HB2      5.339412212   -0.222457558    7.770455360 SER  11     h       H   0.100
+OG       6.989999771   -0.272000015    9.012000084 SER  11     oh      O  -0.380
+HG       6.754035950   -0.477917194    9.993233681 SER  11     ho      H   0.350
+N        4.647999763    3.181999922    7.446000099 ASN  12     n       N  -0.500
+HN       4.830713749    3.344167471    8.446608543 ASN  12     hn      H   0.280
+CA       3.545000076    3.934999943    6.750999928 ASN  12     ca      C   0.120
+HA       2.931945086    3.139469147    6.327450275 ASN  12     h       H   0.100
+C        4.106999874    4.850999832    5.690999985 ASN  12     c'      C   0.380
+O        3.536000013    5.000999928    4.617000103 ASN  12     o'      O  -0.380
+CB       2.663000107    4.677000046    7.748000145 ASN  12     c2      C  -0.200
+HB1      3.340831280    5.294844151    8.336993217 ASN  12     h       H   0.100
+HB2      2.070847750    5.373784065    7.154748440 ASN  12     h       H   0.100
+CG       1.802000046    3.734999895    8.609999657 ASN  12     c'      C   0.380
+OD1      1.567000031    2.612999916    8.164999962 ASN  12     o'      O  -0.380
+ND2      1.394000053    4.251999855    9.767000198 ASN  12     n2      N  -0.560
+HD21     1.661958218    5.212530613   10.024837494 ASN  12     hn      H   0.280
+HD22     0.810311615    3.691485643   10.404206276 ASN  12     hn      H   0.280
+N        5.258999825    5.498000145    6.005000114 PHE  13     n       N  -0.500
+HN       5.665558815    5.373039246    6.943080425 PHE  13     hn      H   0.280
+CA       5.928999901    6.357999802    5.054999828 PHE  13     ca      C   0.120
+HA       5.242126465    7.176824093    4.840915680 PHE  13     h       H   0.100
+C        6.303999901    5.578000069    3.799000025 PHE  13     c'      C   0.380
+O        6.136000156    6.072000027    2.653000116 PHE  13     o'      O  -0.380
+CB       7.183000088    6.993999958    5.754000187 PHE  13     c2      C  -0.200
+HB1      6.822110653    7.422051907    6.689217091 PHE  13     h       H   0.100
+HB2      7.827757359    6.160566807    6.032885551 PHE  13     h       H   0.100
+CG       7.883999825    8.005999565    4.882999897 PHE  13     cp      C   0.000
+CD1      8.906000137    7.585999966    4.026999950 PHE  13     cp      C  -0.100
+HD1      9.200509071    6.536970615    3.996972561 PHE  13     h       H   0.100
+CD2      7.532000065    9.373000145    4.982999802 PHE  13     cp      C  -0.100
+HD2      6.777885437    9.706417084    5.695912361 PHE  13     h       H   0.100
+CE1      9.560000420    8.538999557    3.194000006 PHE  13     cp      C  -0.100
+HE1     10.356478691    8.246096611    2.509945869 PHE  13     h       H   0.100
+CE2      8.175999641   10.281000137    4.144999981 PHE  13     cp      C  -0.100
+HE2      7.907211304   11.336964607    4.173122406 PHE  13     h       H   0.100
+CZ       9.140999794    9.845000267    3.292000055 PHE  13     cp      C  -0.100
+HZ       9.614526749   10.580624580    2.641823530 PHE  13     h       H   0.100
+N        6.900000095    4.389999866    3.989000082 ASN  14     n       N  -0.500
+HN       7.056817055    4.026083469    4.939722538 ASN  14     hn      H   0.280
+CA       7.330999851    3.607000113    2.790999889 ASN  14     ca      C   0.120
+HA       8.025202751    4.266238213    2.269859314 ASN  14     h       H   0.100
+C        6.116000175    3.210000038    1.914999962 ASN  14     c'      C   0.380
+O        6.239999771    3.144000053    0.684000015 ASN  14     o'      O  -0.380
+CB       8.145000458    2.404000044    3.240000010 ASN  14     c2      C  -0.200
+HB1      7.607684612    1.901341796    4.044192791 ASN  14     h       H   0.100
+HB2      8.238607407    1.714848042    2.400710344 ASN  14     h       H   0.100
+CG       9.555000305    2.855999947    3.730000019 ASN  14     c'      C   0.380
+OD1     10.012999535    3.894999981    3.322999954 ASN  14     o'      O  -0.380
+ND2     10.119999886    1.955999970    4.539000034 ASN  14     n2      N  -0.560
+HD21     9.602790833    1.105753064    4.804471970 ASN  14     hn      H   0.280
+HD22    11.072957993    2.112127066    4.897321224 ASN  14     hn      H   0.280
+N        4.993000031    2.927000046    2.571000099 VAL  15     n       N  -0.500
+HN       4.955123901    2.932416916    3.600289106 VAL  15     hn      H   0.280
+CA       3.782000065    2.598999977    1.741999984 VAL  15     ca      C   0.120
+HA       4.121348858    1.813766837    1.066462040 VAL  15     h       H   0.100
+C        3.296000004    3.871000051    1.003999949 VAL  15     c'      C   0.380
+O        2.947000027    3.816999912   -0.188999996 VAL  15     o'      O  -0.380
+CB       2.697999954    1.952999949    2.608000040 VAL  15     c1      C  -0.100
+HB       2.505213737    2.550559521    3.498986244 VAL  15     h       H   0.100
+CG1      1.383999944    1.825999975    1.805999994 VAL  15     c3      C  -0.300
+HG11     0.627347350    1.339950681    2.421900034 VAL  15     h       H   0.100
+HG12     1.035640240    2.818121433    1.518877268 VAL  15     h       H   0.100
+HG13     1.560454965    1.230180860    0.910475850 VAL  15     h       H   0.100
+CG2      3.174000025    0.532999992    3.005000114 VAL  15     c3      C  -0.300
+HG21     3.344338417   -0.058414809    2.105381727 VAL  15     h       H   0.100
+HG22     4.101772785    0.605659664    3.572501659 VAL  15     h       H   0.100
+HG23     2.411232710    0.051358268    3.616807222 VAL  15     h       H   0.100
+N        3.321000099    4.986999989    1.720000029 CYS  16     n       N  -0.500
+HN       3.642014980    4.956790447    2.698231459 CYS  16     hn      H   0.280
+CA       2.890000105    6.284999847    1.126000047 CYS  16     ca      C   0.120
+HA       1.819724441    6.204565048    0.935894310 CYS  16     h       H   0.100
+C        3.687000036    6.597000122   -0.111000001 CYS  16     c'      C   0.380
+O        3.200000048    7.146999836   -1.103000045 CYS  16     o'      O  -0.380
+CB       3.039000034    7.368999958    2.240000010 CYS  16     c2      C  -0.300
+HB1      2.427302361    7.046223164    3.082461596 CYS  16     h       H   0.100
+HB2      4.076938152    7.344151497    2.571914196 CYS  16     h       H   0.100
+SG       2.559000015    9.013999939    1.649000049 CYS  16     s1      S   0.100
+N        4.997000217    6.227000237   -0.100000001 ARG  17     n       N  -0.500
+HN       5.366806507    5.742030144    0.730028629 ARG  17     hn      H   0.280
+CA       5.894999981    6.488999844   -1.213000059 ARG  17     ca      C   0.120
+HA       5.606140137    7.505477905   -1.480268955 ARG  17     h       H   0.100
+C        5.737999916    5.559999943   -2.408999920 ARG  17     c'      C   0.380
+O        6.228000164    5.901000023   -3.506999969 ARG  17     o'      O  -0.380
+CB       7.369999886    6.506999969   -0.731000006 ARG  17     c2      C  -0.200
+HB1      7.554117680    5.576966763   -0.193190947 ARG  17     h       H   0.110
+HB2      8.006169319    6.572014809   -1.613701701 ARG  17     h       H   0.110
+CG       7.717000008    7.686999798    0.206000000 ARG  17     c2      C  -0.200
+HG1      6.892404079    7.845237732    0.901055515 ARG  17     h       H   0.130
+HG2      8.617112160    7.442208767    0.769892812 ARG  17     h       H   0.130
+CD       7.948999882    8.946999550   -0.615000010 ARG  17     c2      C  -0.160
+HD1      7.120620728    9.063755989   -1.313753128 ARG  17     h       H   0.130
+HD2      7.958537579    9.803778648    0.058749799 ARG  17     h       H   0.130
+NE       9.211999893    8.855999947   -1.337000012 ARG  17     n       N  -0.560
+CZ       9.536999702    9.532999992   -2.430999994 ARG  17     cr      C   0.380
+NH1      8.659000397   10.350000381   -3.032000065 ARG  17     n2      N  -0.560
+HH11     7.687877178   10.401560783   -2.692646742 ARG  17     hn      H   0.280
+HH12     8.956042290   10.925786018   -3.832710981 ARG  17     hn      H   0.280
+NH2     10.793000221    9.491000175   -2.898999929 ARG  17     n2      N  -0.560
+HH21    11.487204552    8.872345924   -2.456000090 ARG  17     hn      H   0.280
+HH22    11.063426018   10.077307701   -3.701504469 ARG  17     hn      H   0.280
+N        5.051000118    4.410999775   -2.203999996 LEU  18     n       N  -0.500
+HN       4.617259026    4.215945244   -1.290368676 LEU  18     hn      H   0.280
+CA       4.933000088    3.430999994   -3.325999975 LEU  18     ca      C   0.120
+HA       5.980045319    3.132587433   -3.378404140 LEU  18     h       H   0.100
+C        4.396999836    4.013999939   -4.619999886 LEU  18     c'      C   0.380
+O        4.987999916    3.755000114   -5.686999798 LEU  18     o'      O  -0.380
+CB       4.196000099    2.184000015   -2.862999916 LEU  18     c2      C  -0.200
+HB1      3.339328766    2.530950308   -2.285211325 LEU  18     h       H   0.100
+HB2      3.882649422    1.660040379   -3.765982628 LEU  18     h       H   0.100
+CG       4.960000038    1.177999973   -1.991000056 LEU  18     c1      C  -0.100
+HG       5.379372120    1.654240489   -1.104759574 LEU  18     h       H   0.100
+CD1      3.907000065    0.097000003   -1.633999944 LEU  18     c3      C  -0.300
+HD11     4.372385025   -0.676563323   -1.023166656 LEU  18     h       H   0.100
+HD12     3.089181185    0.555318415   -1.077927470 LEU  18     h       H   0.100
+HD13     3.518241882   -0.348654836   -2.549619913 LEU  18     h       H   0.100
+CD2      6.129000187    0.606000006   -2.767999887 LEU  18     c3      C  -0.300
+HD21     5.767732143    0.166402578   -3.697698832 LEU  18     h       H   0.100
+HD22     6.839241505    1.401178122   -2.994605541 LEU  18     h       H   0.100
+HD23     6.621874809   -0.161501810   -2.171245098 LEU  18     h       H   0.100
+N        3.328999996    4.795000076   -4.543000221 PRO  19     n       N  -0.420
+CA       2.792000055    5.375999928   -5.796999931 PRO  19     ca      C   0.060
+HA       2.750592709    4.562232971   -6.520994663 PRO  19     h       H   0.100
+CD       2.421000004    4.940999985   -3.407999992 PRO  19     c2      C   0.060
+HD1      2.893075705    5.502179623   -2.601574659 PRO  19     h       H   0.100
+HD2      2.129873276    3.967023134   -3.014662504 PRO  19     h       H   0.100
+C        3.572999954    6.539999962   -6.322000027 PRO  19     c'      C   0.380
+O        3.259999990    7.045000076   -7.421999931 PRO  19     o'      O  -0.380
+CB       1.358000040    5.765999794   -5.472000122 PRO  19     c2      C  -0.200
+HB1      1.137144327    6.795158386   -5.755116940 PRO  19     h       H   0.100
+HB2      0.636163235    5.061525822   -5.885241508 PRO  19     h       H   0.100
+CG       1.223000050    5.693999767   -3.993000031 PRO  19     c2      C  -0.200
+HG1      1.192069173    6.702612400   -3.580879211 PRO  19     h       H   0.100
+HG2      0.303467065    5.167813301   -3.736705542 PRO  19     h       H   0.100
+N        4.565000057    7.046999931   -5.559000015 GLY  20     n       N  -0.500
+HN       4.763685703    6.625352859   -4.640502453 GLY  20     hn      H   0.280
+CA       5.366000175    8.190999985   -6.018000126 GLY  20     cg      C   0.020
+HA1      6.411324024    7.914688587   -5.879978657 GLY  20     h       H   0.100
+HA2      5.204787731    8.272821426   -7.092902660 GLY  20     h       H   0.100
+C        5.006999969    9.480999947   -5.280000210 GLY  20     c'      C   0.380
+O        5.534999847   10.510000229   -5.730000019 GLY  20     o'      O  -0.380
+N        4.181000233    9.437999725   -4.262000084 THR  21     n       N  -0.500
+HN       3.805485964    8.521671295   -3.978747845 THR  21     hn      H   0.280
+CA       3.766999960   10.609000206   -3.513000011 THR  21     ca      C   0.120
+HA       3.186850548   11.287978172   -4.137912750 THR  21     h       H   0.100
+C        5.017000198   11.397000313   -3.042000055 THR  21     c'      C   0.380
+O        5.947000027   10.756999969   -2.523000002 THR  21     o'      O  -0.380
+CB       2.992000103   10.187999725   -2.224999905 THR  21     c1      C  -0.070
+HB       3.722551346    9.746408463   -1.547215223 THR  21     h       H   0.100
+OG1      2.051000118    9.144000053   -2.622999907 THR  21     oh      O  -0.380
+HG1      1.135602355    9.567562103   -2.831667185 THR  21     ho      H   0.350
+CG2      2.259999990   11.348999977   -1.550999999 THR  21     c3      C  -0.300
+HG21     1.741620898   10.986124992   -0.663473487 THR  21     h       H   0.100
+HG22     2.980043650   12.114913940   -1.262877345 THR  21     h       H   0.100
+HG23     1.535783529   11.774766922   -2.245502472 THR  21     h       H   0.100
+N        4.971000195   12.703000069   -3.176000118 PRO  22     n       N  -0.420
+CA       6.143000126   13.512999535   -2.696000099 PRO  22     ca      C   0.060
+HA       7.038496494   13.344851494   -3.294257641 PRO  22     h       H   0.100
+CD       3.963999987   13.567000389   -3.811000109 PRO  22     c2      C   0.060
+HD1      3.145355940   13.595741272   -3.091906309 PRO  22     h       H   0.100
+HD2      3.722736835   13.055393219   -4.742746353 PRO  22     h       H   0.100
+C        6.400000095   13.232999802   -1.225000024 PRO  22     c'      C   0.380
+O        5.485000134   13.060999870   -0.381999999 PRO  22     o'      O  -0.380
+CB       5.703000069   14.968999863   -2.920000076 PRO  22     c2      C  -0.200
+HB1      5.180837631   15.406009674   -2.068842649 PRO  22     h       H   0.100
+HB2      6.486554623   15.606681824   -3.329272270 PRO  22     h       H   0.100
+CG       4.676000118   14.892999649   -3.996000051 PRO  22     c2      C  -0.200
+HG1      3.913127184   15.665482521   -3.899067879 PRO  22     h       H   0.100
+HG2      5.117558002   14.866248131   -4.992198467 PRO  22     h       H   0.100
+N        7.728000164   13.296999931   -0.921000004 GLU  23     n       N  -0.500
+HN       8.435604095   13.473001480   -1.648475647 GLU  23     hn      H   0.280
+CA       8.114000320   13.102999687    0.500000000 GLU  23     ca      C   0.120
+HA       7.816065788   12.094260216    0.785972416 GLU  23     h       H   0.100
+C        7.427000046   14.072999954    1.409999967 GLU  23     c'      C   0.380
+O        7.035999775   13.682000160    2.539999962 GLU  23     o'      O  -0.380
+CB       9.647999763   13.284999847    0.660000026 GLU  23     c2      C  -0.200
+HB1      9.905550957   14.228507996    0.178793058 GLU  23     h       H   0.100
+HB2      9.841214180   13.411215782    1.725287557 GLU  23     h       H   0.100
+CG      10.439999580   12.093000412    0.063000001 GLU  23     c2      C  -0.200
+HG1      9.979146957   11.185737610    0.453625947 GLU  23     h       H   0.100
+HG2     10.252198219   12.100539207   -1.010673165 GLU  23     h       H   0.100
+CD      11.940999985   12.170000076    0.391000003 GLU  23     c'      C   0.380
+OE1     12.416000366   13.225000381    0.680999994 GLU  23     o'      O  -0.350
+OE2     12.538999557   11.069999695    0.291999996 GLU  23     oh      O  -0.380
+HE2     11.852339745   10.318097115    0.136945918 GLU  23     ho      H   0.350
+N        7.211999893   15.333999634    0.966000021 ALA  24     n       N  -0.500
+HN       7.454528332   15.605654716    0.002525384 ALA  24     hn      H   0.280
+CA       6.613999844   16.316999435    1.912999988 ALA  24     ca      C   0.120
+HA       7.281579018   16.350204468    2.774008274 ALA  24     h       H   0.100
+C        5.211999893   15.935999870    2.349999905 ALA  24     c'      C   0.380
+O        4.782000065   16.166000366    3.494999886 ALA  24     o'      O  -0.380
+CB       6.605000019   17.694999695    1.246000051 ALA  24     c3      C  -0.300
+HB1      6.237848759   18.439016342    1.952922821 ALA  24     h       H   0.100
+HB2      7.617130280   17.956361771    0.937162876 ALA  24     h       H   0.100
+HB3      5.953601360   17.672107697    0.372354269 ALA  24     h       H   0.100
+N        4.445000172   15.317999840    1.404999971 ILE  25     n       N  -0.500
+HN       4.817237854   15.149471283    0.459517360 ILE  25     hn      H   0.280
+CA       3.073999882   14.894000053    1.756000042 ILE  25     ca      C   0.120
+HA       2.651019573   15.738821983    2.299565554 ILE  25     h       H   0.100
+C        3.085000038   13.642999649    2.644999981 ILE  25     c'      C   0.380
+O        2.315000057   13.522999763    3.578000069 ILE  25     o'      O  -0.380
+CB       2.203999996   14.637000084    0.462000012 ILE  25     c1      C  -0.100
+HB       2.766484499   14.064008713   -0.275151134 ILE  25     h       H   0.100
+CG1      1.815000057   16.048000336   -0.128999993 ILE  25     c2      C  -0.200
+HG11     2.730222702   16.635150909   -0.204643890 ILE  25     h       H   0.100
+HG12     1.443681121   15.888158798   -1.141261339 ILE  25     h       H   0.100
+CG2      0.902999997   13.864000320    0.810999990 ILE  25     c3      C  -0.300
+HG21     0.304098606   13.734000206   -0.090398379 ILE  25     h       H   0.100
+HG22     1.159095764   12.886850357    1.220502138 ILE  25     h       H   0.100
+HG23     0.331401974   14.427850723    1.548189402 ILE  25     h       H   0.100
+CD1      0.755999982   16.760999680    0.757000029 ILE  25     c3      C  -0.300
+HD11     1.158126354   16.905153275    1.759802103 ILE  25     h       H   0.100
+HD12     0.510290921   17.729721069    0.321907312 ILE  25     h       H   0.100
+HD13    -0.144283146   16.148948669    0.811632454 ILE  25     h       H   0.100
+N        4.032000065   12.763999939    2.312999964 CYS  26     n       N  -0.500
+HN       4.636651039   12.911288261    1.492266655 CYS  26     hn      H   0.280
+CA       4.179999828   11.548999786    3.187000036 CYS  26     ca      C   0.120
+HA       3.168948889   11.146821976    3.251257181 CYS  26     h       H   0.100
+C        4.631999969   11.944000244    4.596000195 CYS  26     c'      C   0.380
+O        4.227000237   11.251999855    5.546999931 CYS  26     o'      O  -0.380
+CB       5.038000107   10.517999649    2.539000034 CYS  26     c2      C  -0.300
+HB1      5.986673355   10.992624283    2.288298368 CYS  26     h       H   0.100
+HB2      5.186637402    9.715300560    3.261275530 CYS  26     h       H   0.100
+SG       4.348999977    9.793999672    1.021999955 CYS  26     s1      S   0.100
+N        5.407999992   13.012000084    4.693999767 ALA  27     n       N  -0.500
+HN       5.691634178   13.513016701    3.839930773 ALA  27     hn      H   0.280
+CA       5.879000187   13.501999855    6.026000023 ALA  27     ca      C   0.120
+HA       6.445541859   12.670074463    6.444367886 ALA  27     h       H   0.100
+C        4.696000099   13.907999992    6.881999969 ALA  27     c'      C   0.380
+O        4.527999878   13.421999931    8.024999619 ALA  27     o'      O  -0.380
+CB       6.880000114   14.614999771    5.829999924 ALA  27     c3      C  -0.300
+HB1      7.267490864   14.930619240    6.798676968 ALA  27     h       H   0.100
+HB2      7.702079296   14.259757042    5.208639622 ALA  27     h       H   0.100
+HB3      6.394177914   15.459349632    5.340969563 ALA  27     h       H   0.100
+N        3.826999903   14.802000046    6.357999802 THR  28     n       N  -0.500
+HN       3.955853701   15.176399231    5.407146454 THR  28     hn      H   0.280
+CA       2.690999985   15.220999718    7.193999767 THR  28     ca      C   0.120
+HA       3.191283464   15.484881401    8.125762939 THR  28     h       H   0.100
+C        1.672000051   14.131999969    7.434000015 THR  28     c'      C   0.380
+O        0.947000027   14.112000465    8.468000412 THR  28     o'      O  -0.380
+CB       1.985999942   16.520000458    6.613999844 THR  28     c1      C  -0.070
+HB       1.055821180   16.708566666    7.150013447 THR  28     h       H   0.100
+OG1      1.664000034   16.221000671    5.230000019 THR  28     oh      O  -0.380
+HG1      1.387834191   17.087430954    4.746335030 THR  28     ho      H   0.350
+CG2      2.914000034   17.739000320    6.699999809 THR  28     c3      C  -0.300
+HG21     2.420290470   18.604087830    6.257310867 THR  28     h       H   0.100
+HG22     3.144372940   17.947925568    7.744690895 THR  28     h       H   0.100
+HG23     3.837480545   17.532133102    6.159175873 THR  28     h       H   0.100
+N        1.621000051   13.189999580    6.511000156 TYR  29     n       N  -0.500
+HN       2.223951578   13.259345055    5.678810120 TYR  29     hn      H   0.280
+CA       0.714999974   12.045000076    6.657000065 TYR  29     ca      C   0.120
+HA      -0.294524491   12.413607597    6.838903904 TYR  29     h       H   0.100
+C        1.125000000   11.125000000    7.815000057 TYR  29     c'      C   0.380
+O        0.286000013   10.631999969    8.545000076 TYR  29     o'      O  -0.380
+CB       0.754999995   11.229000092    5.322000027 TYR  29     c2      C  -0.200
+HB1      0.514248192   11.922528267    4.516296864 TYR  29     h       H   0.100
+HB2      1.786919236   10.911371231    5.172484398 TYR  29     h       H   0.100
+CG      -0.202999994   10.043999672    5.354000092 TYR  29     cp      C   0.000
+CD1     -1.547000051   10.336999893    5.644999981 TYR  29     cp      C  -0.100
+HD1     -1.844175816   11.365451813    5.850120068 TYR  29     h       H   0.100
+CD2      0.193000004    8.750000000    5.099999905 TYR  29     cp      C  -0.100
+HD2      1.231727839    8.520407677    4.862445831 TYR  29     h       H   0.100
+CE1     -2.496000051    9.329000473    5.672999859 TYR  29     cp      C  -0.100
+HE1     -3.542724609    9.551148415    5.880649567 TYR  29     h       H   0.100
+CE2     -0.800999999    7.704999924    5.156000137 TYR  29     cp      C  -0.100
+HE2     -0.521442473    6.666428089    4.979036331 TYR  29     h       H   0.100
+CZ      -2.078999996    8.031000137    5.429999828 TYR  29     cp      C   0.030
+OH      -3.096999884    7.057000160    5.458000183 TYR  29     oh      O  -0.380
+HH      -4.016462326    7.520978928    5.472573757 TYR  29     ho      H   0.350
+N        2.470000029   10.984000206    7.994999886 THR  30     n       N  -0.500
+HN       3.124760151   11.572608948    7.460463524 THR  30     hn      H   0.280
+CA       2.986000061    9.994000435    8.949999809 THR  30     ca      C   0.120
+HA       2.109365702    9.410336494    9.230978012 THR  30     h       H   0.100
+C        3.608999968   10.505000114   10.229999542 THR  30     c'      C   0.380
+O        3.766000032    9.715000153   11.185999870 THR  30     o'      O  -0.380
+CB       4.076000214    9.102999687    8.225000381 THR  30     c1      C  -0.070
+HB       4.516047001    8.447491646    8.976511002 THR  30     h       H   0.100
+OG1      5.125000000   10.027000427    7.823999882 THR  30     oh      O  -0.380
+HG1      5.989885330    9.809993744    8.339540482 THR  30     ho      H   0.350
+CG2      3.493000031    8.324000359    7.034999847 THR  30     c3      C  -0.300
+HG21     4.283595562    7.746788025    6.555538177 THR  30     h       H   0.100
+HG22     2.714145184    7.648486614    7.388787270 THR  30     h       H   0.100
+HG23     3.067262888    9.023551941    6.315641403 THR  30     h       H   0.100
+N        3.983999968   11.763999939   10.241000175 GLY  31     n       N  -0.500
+HN       3.725119591   12.370410919    9.449706078 GLY  31     hn      H   0.280
+CA       4.769000053   12.336000443   11.359999657 GLY  31     cg      C   0.020
+HA1      4.444449425   13.369131088   11.484130859 GLY  31     h       H   0.100
+HA2      4.479221344   11.798232079   12.262736320 GLY  31     h       H   0.100
+C        6.255000114   12.243000031   11.105999947 GLY  31     c'      C   0.380
+O        7.037000179   12.750000000   11.954000473 GLY  31     o'      O  -0.380
+N        6.710000038   11.630999565    9.991999626 CYS  32     n       N  -0.500
+HN       6.054100990   11.116460800    9.387064934 CYS  32     hn      H   0.280
+CA       8.140000343   11.694000244    9.635000229 CYS  32     ca      C   0.120
+HA       8.678412437   11.410507202   10.539347649 CYS  32     h       H   0.100
+C        8.500000000   13.140999794    9.206000328 CYS  32     c'      C   0.380
+O        7.580999851   13.949000359    8.944000244 CYS  32     o'      O  -0.380
+CB       8.503999710   10.685999870    8.529999733 CYS  32     c2      C  -0.300
+HB1      7.987734795   10.995699883    7.621343136 CYS  32     h       H   0.100
+HB2      9.584586143   10.726516724    8.392916679 CYS  32     h       H   0.100
+SG       8.048000336    8.987000465    8.880999565 CYS  32     s1      S   0.100
+N        9.793000221   13.409999847    9.173000336 ILE  33     n       N  -0.500
+HN      10.471553802   12.667460442    9.394585609 ILE  33     hn      H   0.280
+CA      10.279999733   14.760000229    8.822999954 ILE  33     ca      C   0.120
+HA       9.389740944   15.283022881    8.473735809 ILE  33     h       H   0.100
+C       11.345999718   14.657999992    7.743000031 ILE  33     c'      C   0.380
+O       11.970999718   13.583000183    7.552000046 ILE  33     o'      O  -0.380
+CB      10.789999962   15.534999847   10.085000038 ILE  33     c1      C  -0.100
+HB      11.123229027   16.501873016    9.707884789 ILE  33     h       H   0.100
+CG1     12.059000015   14.803000450   10.670999527 ILE  33     c2      C  -0.200
+HG11    11.743847847   13.842393875   11.078448296 ILE  33     h       H   0.100
+HG12    12.756343842   14.617484093    9.854057312 ILE  33     h       H   0.100
+CG2      9.684000015   15.685999870   11.137999535 ILE  33     c3      C  -0.300
+HG21    10.058896065   16.270494461   11.978191376 ILE  33     h       H   0.100
+HG22     8.827452660   16.194667816   10.695638657 ILE  33     h       H   0.100
+HG23     9.378940582   14.700247765   11.489184380 ILE  33     h       H   0.100
+CD1     12.732999802   15.675999641   11.781000137 ILE  33     c3      C  -0.300
+HD11    12.021772385   15.850844383   12.588270187 ILE  33     h       H   0.100
+HD12    13.606328964   15.155009270   12.173381805 ILE  33     h       H   0.100
+HD13    13.041068077   16.631135941   11.355658531 ILE  33     h       H   0.100
+N       11.489999771   15.772999763    7.038000107 ILE  34     n       N  -0.500
+HN      10.853153229   16.566915512    7.196191311 ILE  34     hn      H   0.280
+CA      12.552000046   15.876999855    6.035999775 ILE  34     ca      C   0.120
+HA      13.043725967   14.912866592    5.906565666 ILE  34     h       H   0.100
+C       13.590000153   16.916999817    6.559999943 ILE  34     c'      C   0.380
+O       13.168000221   18.006000519    6.945000172 ILE  34     o'      O  -0.380
+CB      11.987000465   16.360000610    4.681000233 ILE  34     c1      C  -0.100
+HB      11.502662659   17.321004868    4.854168892 ILE  34     h       H   0.100
+CG1     10.913999557   15.338000298    4.163000107 ILE  34     c2      C  -0.200
+HG11    11.380437851   14.426782608    3.788544178 ILE  34     h       H   0.100
+HG12    10.170696259   15.118617058    4.929467201 ILE  34     h       H   0.100
+CG2     13.130999565   16.517000198    3.628999949 ILE  34     c3      C  -0.300
+HG21    12.714348793   16.881505966    2.690041304 ILE  34     h       H   0.100
+HG22    13.869889259   17.228136063    3.998366594 ILE  34     h       H   0.100
+HG23    13.608166695   15.551076889    3.463472128 ILE  34     h       H   0.100
+CD1     10.151000023   16.024000168    2.937999964 ILE  34     c3      C  -0.300
+HD11    10.865941048   16.258329391    2.149300337 ILE  34     h       H   0.100
+HD12     9.395269394   15.340338707    2.551244020 ILE  34     h       H   0.100
+HD13     9.670580864   16.941936493    3.276658058 ILE  34     h       H   0.100
+N       14.855999947   16.493000031    6.535999775 ILE  35     n       N  -0.500
+HN      15.087069511   15.531770706    6.246958256 ILE  35     hn      H   0.280
+CA      15.930000305   17.454000473    6.940999985 ILE  35     ca      C   0.120
+HA      15.448633194   18.412040710    7.137327194 ILE  35     h       H   0.100
+C       16.913000107   17.549999237    5.818999767 ILE  35     c'      C   0.380
+O       17.097000122   16.659999847    4.969999790 ILE  35     o'      O  -0.380
+CB      16.621999741   16.995000839    8.284999847 ILE  35     c1      C  -0.100
+HB      17.372821808   17.751832962    8.512095451 ILE  35     h       H   0.100
+CG1     17.360000610   15.651000023    8.067000389 ILE  35     c2      C  -0.200
+HG11    16.597890854   14.882443428    7.938127518 ILE  35     h       H   0.100
+HG12    17.962522507   15.757192612    7.164896488 ILE  35     h       H   0.100
+CG2     15.592000008   16.974000931    9.434000015 ILE  35     c3      C  -0.300
+HG21    16.095645905   16.731447220   10.369737625 ILE  35     h       H   0.100
+HG22    15.121275902   17.953468323    9.518616676 ILE  35     h       H   0.100
+HG23    14.830537796   16.222230911    9.226348877 ILE  35     h       H   0.100
+CD1     18.298000336   15.206000328    9.218999863 ILE  35     c3      C  -0.300
+HD11    17.719526291   15.091951370   10.135765076 ILE  35     h       H   0.100
+HD12    18.762899399   14.254055977    8.962544441 ILE  35     h       H   0.100
+HD13    19.071800232   15.958778381    9.369535446 ILE  35     h       H   0.100
+N       17.663999557   18.669000626    5.806000233 PRO  36     n       N  -0.420
+CA      18.635000229   18.861000061    4.737999916 PRO  36     ca      C   0.060
+HA      18.191711426   18.625682831    3.770414352 PRO  36     h       H   0.100
+CD      17.371000290   19.899999619    6.596000195 PRO  36     c2      C   0.060
+HD1     17.637220383   19.770334244    7.645006180 PRO  36     h       H   0.100
+HD2     16.312007904   20.154773712    6.554459572 PRO  36     h       H   0.100
+C       19.924999237   18.041999817    4.948999882 PRO  36     c'      C   0.380
+O       20.593000412   17.742000580    3.944999933 PRO  36     o'      O  -0.380
+CB      18.944999695   20.364000320    4.782999992 PRO  36     c2      C  -0.200
+HB1     20.011636734   20.533958435    4.929625034 PRO  36     h       H   0.100
+HB2     18.596609116   20.857370377    3.875635624 PRO  36     h       H   0.100
+CG      18.238000870   20.937000275    5.907999992 PRO  36     c2      C  -0.200
+HG1     18.980670929   21.346309662    6.592840672 PRO  36     h       H   0.100
+HG2     17.637973785   21.766929626    5.534794807 PRO  36     h       H   0.100
+N       20.172000885   17.729999542    6.217000008 GLY  37     n       N  -0.500
+HN      19.520402908   17.994186401    6.969678879 GLY  37     hn      H   0.280
+CA      21.451999664   16.968999863    6.513000011 GLY  37     cg      C   0.020
+HA1     22.220170975   17.196077347    5.773777485 GLY  37     h       H   0.100
+HA2     21.806970596   17.180898666    7.521560192 GLY  37     h       H   0.100
+C       21.142999649   15.477999687    6.427000046 GLY  37     c'      C   0.380
+O       20.138000488   15.022999763    5.877999783 GLY  37     o'      O  -0.380
+N       22.055000305   14.701000214    7.032000065 ALA  38     n       N  -0.500
+HN      22.826601028   15.162067413    7.534940720 ALA  38     hn      H   0.280
+CA      22.018999100   13.241999626    7.019999981 ALA  38     ca      C   0.120
+HA      21.118928909   12.994981766    6.457010269 ALA  38     h       H   0.100
+C       21.944000244   12.628000259    8.395999908 ALA  38     c'      C   0.380
+O       21.868999481   11.387000084    8.435000420 ALA  38     o'      O  -0.380
+CB      23.246000290   12.696999550    6.275000095 ALA  38     c3      C  -0.300
+HB1     23.164216995   11.613998413    6.182674408 ALA  38     h       H   0.100
+HB2     23.296331406   13.143034935    5.281710148 ALA  38     h       H   0.100
+HB3     24.149721146   12.946521759    6.830985546 ALA  38     h       H   0.100
+N       21.893999100   13.435000420    9.435999870 THR  39     n       N  -0.500
+HN      21.824220657   14.451409340    9.284524918 THR  39     hn      H   0.280
+CA      21.936000824   12.911000252   10.809000015 THR  39     ca      C   0.120
+HA      22.114582062   11.836632729   10.764920235 THR  39     h       H   0.100
+C       20.614999771   13.190999985   11.520999908 THR  39     c'      C   0.380
+O       20.357000351   14.317000389   11.947999954 THR  39     o'      O  -0.380
+CB      23.131000519   13.600999832   11.593000412 THR  39     c1      C  -0.070
+HB      22.981323242   14.676721573   11.685302734 THR  39     h       H   0.100
+OG1     24.284000397   13.401000023   10.708999634 THR  39     oh      O  -0.380
+HG1     24.421899796   14.240586281   10.128500938 THR  39     ho      H   0.350
+CG2     23.340000153   12.935000420   12.961999893 THR  39     c3      C  -0.300
+HG21    24.219049454   13.362584114   13.444229126 THR  39     h       H   0.100
+HG22    22.463815689   13.106077194   13.587406158 THR  39     h       H   0.100
+HG23    23.485591888   11.863260269   12.826802254 THR  39     h       H   0.100
+N       19.826999664   12.109999657   11.642000198 CYS  40     n       N  -0.500
+HN      20.122940063   11.185415268   11.297814369 CYS  40     hn      H   0.280
+CA      18.503999710   12.312000275   12.298000336 CYS  40     ca      C   0.120
+HA      18.057098389   13.220839500   11.895023346 CYS  40     h       H   0.100
+C       18.684000015   12.451000214   13.784000397 CYS  40     c'      C   0.380
+O       19.533000946   11.718000412   14.362000465 CYS  40     o'      O  -0.380
+CB      17.582000732   11.116999626   11.996000290 CYS  40     c2      C  -0.300
+HB1     18.086227417   10.251184464   12.425209045 CYS  40     h       H   0.100
+HB2     16.700305939   11.271791458   12.617895126 CYS  40     h       H   0.100
+SG      17.198999405   10.928999901   10.237000465 CYS  40     s1      S   0.100
+N       17.879999161   13.265999794   14.425999641 PRO  41     n       N  -0.420
+CA      17.923999786   13.420999527   15.876999855 PRO  41     ca      C   0.060
+HA      18.941534042   13.662834167   16.183986664 PRO  41     h       H   0.100
+CD      16.858999252   14.149999619   13.779000282 PRO  41     c2      C   0.060
+HD1     16.215919495   13.587250710   13.102345467 PRO  41     h       H   0.100
+HD2     17.329374313   14.943244934   13.197958946 PRO  41     h       H   0.100
+C       17.392000198   12.206000328   16.593999863 PRO  41     c'      C   0.380
+O       16.652000427   11.368000031   16.033000946 PRO  41     o'      O  -0.380
+CB      17.076000214   14.657999992   16.145000458 PRO  41     c2      C  -0.200
+HB1     16.444255829   14.584781647   17.030233383 PRO  41     h       H   0.100
+HB2     17.617696762   15.599854469   16.057970047 PRO  41     h       H   0.100
+CG      16.097999573   14.689000130   14.996999741 PRO  41     c2      C  -0.200
+HG1     15.253420830   14.016077042   15.145191193 PRO  41     h       H   0.100
+HG2     15.789084435   15.700772285   14.734343529 PRO  41     h       H   0.100
+N       17.728000641   12.123999596   17.884000778 GLY  42     n       N  -0.500
+HN      18.268247604   12.885299683   18.319267273 GLY  42     hn      H   0.280
+CA      17.333999634   10.956000328   18.690999985 GLY  42     cg      C   0.020
+HA1     17.766984940   10.084270477   18.200376511 GLY  42     h       H   0.100
+HA2     17.761390686   11.109748840   19.681858063 GLY  42     h       H   0.100
+C       15.875000000   10.687999725   18.871000290 GLY  42     c'      C   0.380
+O       15.434000015    9.550000191   19.166000366 GLY  42     o'      O  -0.380
+N       15.036000252   11.746999741   18.715000153 ASP  43     n       N  -0.500
+HN      15.424054146   12.679033279   18.510971069 ASP  43     hn      H   0.280
+CA      13.564000130   11.572999954   18.836000443 ASP  43     ca      C   0.120
+HA      13.474464417   10.696401596   19.477605820 ASP  43     h       H   0.100
+C       12.935999870   11.227000237   17.469999313 ASP  43     c'      C   0.380
+O       11.720000267   11.039999962   17.427999496 ASP  43     o'      O  -0.380
+CB      12.932999611   12.737000465   19.579999924 ASP  43     c2      C  -0.200
+HB1     11.860553741   12.547567368   19.625556946 ASP  43     h       H   0.100
+HB2     13.367670059   12.754883766   20.579420090 ASP  43     h       H   0.100
+CG      13.140000343   14.093999863   18.958000183 ASP  43     c'      C   0.380
+OD1     14.109000206   14.303000450   18.211999893 ASP  43     o'      O  -0.350
+OD2     12.267000198   14.963000298   19.264999390 ASP  43     oh      O  -0.380
+HD2     12.695192337   15.899699211   19.252908707 ASP  43     ho      H   0.350
+N       13.725000381   11.173999786   16.424999237 TYR  44     n       N  -0.500
+HN      14.713005066   11.441411018   16.540052414 TYR  44     hn      H   0.280
+CA      13.256999969   10.744999886   15.081000328 TYR  44     ca      C   0.120
+HA      12.264418602   10.301728249   15.160951614 TYR  44     h       H   0.100
+C       14.274999619    9.687000275   14.612000465 TYR  44     c'      C   0.380
+O       14.930000305    9.862000465   13.567999840 TYR  44     o'      O  -0.380
+CB      13.199999809   11.913999557   14.071000099 TYR  44     c2      C  -0.200
+HB1     14.121270180   12.493051529   14.134719849 TYR  44     h       H   0.100
+HB2     13.091276169   11.516075134   13.062071800 TYR  44     h       H   0.100
+CG      12.000000000   12.819000244   14.399000168 TYR  44     cp      C   0.000
+CD1     12.119000435   13.852999687   15.331999779 TYR  44     cp      C  -0.100
+HD1     13.067806244   14.011770248   15.844503403 TYR  44     h       H   0.100
+CD2     10.774999619   12.616999626   13.762000084 TYR  44     cp      C  -0.100
+HD2     10.673528671   11.813380241   13.032616615 TYR  44     h       H   0.100
+CE1     11.045000076   14.675000191   15.609999657 TYR  44     cp      C  -0.100
+HE1     11.163392067   15.500525475   16.311847687 TYR  44     h       H   0.100
+CE2      9.675999641   13.432999611   14.048000336 TYR  44     cp      C  -0.100
+HE2      8.726944923   13.273748398   13.536108017 TYR  44     h       H   0.100
+CZ       9.802000046   14.456000328   14.996000290 TYR  44     cp      C   0.030
+OH       8.739999771   15.265000343   15.269000053 TYR  44     oh      O  -0.380
+HH       9.048466682   16.247716904   15.272980690 TYR  44     ho      H   0.350
+N       14.342000008    8.640000343   15.421999931 ALA  45     n       N  -0.500
+HN      13.638368607    8.505084991   16.162000656 ALA  45     hn      H   0.280
+CA      15.444999695    7.666999817   15.246000290 ALA  45     ca      C   0.120
+HA      16.332574844    8.216528893   14.932426453 ALA  45     h       H   0.100
+C       15.170999527    6.532999992   14.279999733 ALA  45     c'      C   0.380
+O       16.093000412    5.704999924   14.038999557 ALA  45     o'      O  -0.380
+CB      15.680000305    7.098999977   16.681999207 ALA  45     c3      C  -0.300
+HB1     16.535034180    6.423069000   16.670495987 ALA  45     h       H   0.100
+HB2     15.876356125    7.920741558   17.370683670 ALA  45     h       H   0.100
+HB3     14.792826653    6.556271553   17.008296967 ALA  45     h       H   0.100
+N       13.965999603    6.501999855   13.739000320 ASNC 46     n       N  -0.500
+HN      13.318986893    7.281283855   13.926057816 ASNC 46     hn      H   0.280
+CA      13.512000084    5.394999981   12.878000259 ASNC 46     ca      C   0.120
+HA      14.292015076    4.641647816   12.988171577 ASNC 46     h       H   0.100
+C       13.310999870    5.853000164   11.454999924 ASNC 46     c-      C   0.140
+O       13.732999802    6.928999901   11.026000023 ASNC 46     o-      O  -0.570
+OXT     12.703000069    4.973000050   10.746000290 ASNC 46     o-      O  -0.570
+CB      12.265999794    4.769000053   13.501000404 ASNC 46     c2      C  -0.200
+HB1     11.471806526    5.515164375   13.476576805 ASNC 46     h       H   0.100
+HB2     11.959742546    3.937092304   12.866779327 ASNC 46     h       H   0.100
+CG      12.538000107    4.303999901   14.921999931 ASNC 46     c'      C   0.380
+OD1     11.982000351    4.848999977   15.885999680 ASNC 46     o'      O  -0.380
+ND2     13.406999588    3.298000097   15.015000343 ASNC 46     n2      N  -0.560
+HD21    13.826193810    2.899175167   14.162875175 ASNC 46     hn      H   0.280
+HD22    13.659525871    2.919377804   15.938999176 ASNC 46     hn      H   0.280
+end                                                                             
+end                                                                             
+

tools/msi2lmp/test/crambin.mdf

@@ -0,0 +1,840 @@
+!BIOSYM molecular_data 4
+
+!DATE:      Mon Jul 14 13:41:24 1997     INSIGHT generated molecular data file 
+
+#topology                                                                      
+
+@column 1 element                                                              
+@column 2 atom_type cvff                                                       
+@column 3 charge_group cvff                                                    
+@column 4 isotope                                                              
+@column 5 formal_charge                                                        
+@column 6 charge cvff                                                          
+@column 7 switching_atom cvff                                                  
+@column 8 oop_flag cvff                                                        
+@column 9 chirality_flag                                                       
+@column 10 occupancy                                                           
+@column 11 xray_temp_factor                                                    
+@column 12 connections                                                         
+
+@molecule CRAMBIN                                                             
+
+THRN_1:N            N  n4      pep+ 0  0  -0.5000 1 0 8  1.0000 13.7900 CA HN1 HN2 HN3 
+THRN_1:HN3          H  hn      pep+ 0  0   0.3600 0 0 8  1.0000  0.0000 N 
+THRN_1:HN1          H  hn      pep+ 0  0   0.3600 0 0 8  1.0000  0.0000 N 
+THRN_1:HN2          H  hn      pep+ 0  0   0.3600 0 0 8  1.0000  0.0000 N 
+THRN_1:CA           C  ca      pep+ 0  0   0.3200 0 0 8  1.0000 10.8000 C CB N HA 
+THRN_1:HA           H  h       pep+ 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THRN_1:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  9.1900 O/2.0 CA THR_2:N/1.5 
+THRN_1:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.8500 C/2.0 
+THRN_1:CB           C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000 13.0200 CG2 OG1 CA HB 
+THRN_1:HB           H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THRN_1:OG1          O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000 15.0600 CB HG1 
+THRN_1:HG1          H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THRN_1:CG2          C  c3      meG  0  0  -0.3000 1 0 8  1.0000 14.2300 CB HG21 HG22 HG23 
+THRN_1:HG21         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THRN_1:HG22         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THRN_1:HG23         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_2:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  7.8100 CA THRN_1:C/1.5 HN 
+THR_2:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+THR_2:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  8.3100 C CB N HA 
+THR_2:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THR_2:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.8000 O/2.0 CA CYS_3:N/1.5 
+THR_2:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.9400 C/2.0 
+THR_2:CB            C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000 10.3200 CG2 OG1 CA HB 
+THR_2:HB            H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_2:OG1           O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000 12.8100 CB HG1 
+THR_2:HG1           H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THR_2:CG2           C  c3      meG  0  0  -0.3000 1 0 8  1.0000 11.9000 CB HG21 HG22 HG23 
+THR_2:HG21          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_2:HG22          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_2:HG23          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+CYS_3:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.2400 CA THR_2:C/1.5 HN 
+CYS_3:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_3:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.3900 C CB N HA 
+CYS_3:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_3:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.4500 O/2.0 CA CYS_4:N/1.5 
+CYS_3:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.5400 C/2.0 
+CYS_3:CB            C  c2      cs   0  0  -0.3000 1 0 8  1.0000  5.9900 SG CA HB1 HB2 
+CYS_3:HB1           H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_3:HB2           H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_3:SG            S  s1      cs   0  0   0.1000 0 0 8  1.0000  7.0100 CB CYS_40:SG 
+CYS_4:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.9000 CA CYS_3:C/1.5 HN 
+CYS_4:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_4:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.2400 C CB N HA 
+CYS_4:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_4:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.7200 O/2.0 CA PRO_5:N/1.5 
+CYS_4:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.3000 C/2.0 
+CYS_4:CB            C  c2      cs   0  0  -0.3000 1 0 8  1.0000  4.4100 SG CA HB1 HB2 
+CYS_4:HB1           H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_4:HB2           H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_4:SG            S  s1      cs   0  0   0.1000 0 0 8  1.0000  4.7200 CB CYS_32:SG 
+PRO_5:N             N  n       pepN 0  0  -0.4200 1 1 8  1.0000  3.9600 CA CD CYS_4:C/1.5 
+PRO_5:CA            C  ca      pepN 0  0   0.0600 0 0 8  1.0000  4.2500 C CB N HA 
+PRO_5:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PRO_5:CD            C  c2      pepN 0  0   0.0600 0 0 8  1.0000  5.2000 N CG HD1 HD2 
+PRO_5:HD1           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_5:HD2           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_5:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.9600 O/2.0 CA SER_6:N/1.5 
+PRO_5:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.4400 C/2.0 
+PRO_5:CB            C  c2      meB  0  0  -0.2000 1 0 8  1.0000  5.1100 CG CA HB1 HB2 
+PRO_5:HB1           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_5:HB2           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_5:CG            C  c2      meG  0  0  -0.2000 1 0 8  1.0000  5.2400 CD CB HG1 HG2 
+PRO_5:HG1           H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+PRO_5:HG2           H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+SER_6:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.8300 CA PRO_5:C/1.5 HN 
+SER_6:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+SER_6:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.4500 C CB N HA 
+SER_6:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+SER_6:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.9900 O/2.0 CA ILE_7:N/1.5 
+SER_6:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.6100 C/2.0 
+SER_6:CB            C  c2      coh  0  0  -0.1700 0 0 8  1.0000  5.0500 OG CA HB1 HB2 
+SER_6:HB1           H  h       coh  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+SER_6:HB2           H  h       coh  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+SER_6:OG            O  oh      coh  0  0  -0.3800 1 0 8  1.0000  6.3900 CB HG 
+SER_6:HG            H  ho      coh  0  0   0.3500 0 0 8  1.0000  0.0000 OG 
+ILE_7:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.9400 CA SER_6:C/1.5 HN 
+ILE_7:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ILE_7:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  6.3300 C CB N HA 
+ILE_7:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ILE_7:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.3200 O/2.0 CA VAL_8:N/1.5 
+ILE_7:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.8500 C/2.0 
+ILE_7:CB            C  c1      meB  0  0  -0.1000 1 0 8  1.0000  8.4300 CG2 CG1 CA HB 
+ILE_7:HB            H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_7:CG1           C  c2      meG1 0  0  -0.2000 1 0 8  1.0000  9.7800 CD1 CB HG11 HG12 
+ILE_7:HG11          H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_7:HG12          H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_7:CG2           C  c3      meG2 0  0  -0.3000 1 0 8  1.0000 11.7000 CB HG21 HG22 HG23 
+ILE_7:HG21          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_7:HG22          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_7:HG23          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_7:CD1           C  c3      meD1 0  0  -0.3000 1 0 8  1.0000  9.9200 CG1 HD11 HD12 HD13 
+ILE_7:HD11          H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_7:HD12          H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_7:HD13          H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+VAL_8:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.0200 CA ILE_7:C/1.5 HN 
+VAL_8:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+VAL_8:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  6.9300 C CB N HA 
+VAL_8:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+VAL_8:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.3900 O/2.0 CA ALA_9:N/1.5 
+VAL_8:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.3000 C/2.0 
+VAL_8:CB            C  c1      meB  0  0  -0.1000 1 0 8  1.0000  9.6400 CG1 CG2 CA HB 
+VAL_8:HB            H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+VAL_8:CG1           C  c3      meG1 0  0  -0.3000 1 0 8  1.0000 13.8500 CB HG11 HG12 HG13 
+VAL_8:HG11          H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_8:HG12          H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_8:HG13          H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_8:CG2           C  c3      meG2 0  0  -0.3000 1 0 8  1.0000 11.9700 CB HG21 HG22 HG23 
+VAL_8:HG21          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+VAL_8:HG22          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+VAL_8:HG23          H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ALA_9:N             N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.7300 CA VAL_8:C/1.5 HN 
+ALA_9:HN            H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ALA_9:CA            C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.5600 C CB N HA 
+ALA_9:HA            H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ALA_9:C             C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1300 O/2.0 CA ARG_10:N/1.5 
+ALA_9:O             O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.3600 C/2.0 
+ALA_9:CB            C  c3      meB  0  0  -0.3000 1 0 8  1.0000  4.8000 CA HB1 HB2 HB3 
+ALA_9:HB1           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_9:HB2           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_9:HB3           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ARG_10:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.7300 CA ALA_9:C/1.5 HN 
+ARG_10:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ARG_10:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.3800 C CB N HA 
+ARG_10:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ARG_10:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.4700 O/2.0 CA SER_11:N/1.5 
+ARG_10:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.6700 C/2.0 
+ARG_10:CB           C  c2      c3nc 0  0  -0.2000 0 0 8  1.0000  3.9500 CG CA HB1 HB2 
+ARG_10:HB1          H  h       c3nc 0  0   0.1100 0 0 8  1.0000  0.0000 CB 
+ARG_10:HB2          H  h       c3nc 0  0   0.1100 0 0 8  1.0000  0.0000 CB 
+ARG_10:CG           C  c2      c3nc 0  0  -0.2000 0 0 8  1.0000  4.5500 CD CB HG1 HG2 
+ARG_10:HG1          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CG 
+ARG_10:HG2          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CG 
+ARG_10:CD           C  c2      c3nc 0  0  -0.1600 1 0 8  1.0000  5.8900 NE CG HD1 HD2 
+ARG_10:HD1          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CD 
+ARG_10:HD2          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CD 
+ARG_10:NE           N  n       c3nc 0  0  -0.5600 0 0 8  1.0000  6.2000 CZ/2.0 CD 
+ARG_10:CZ           C  cr      c3nc 0  0   0.3800 0 1 8  1.0000  7.5200 NH1 NH2 NE/2.0 
+ARG_10:NH1          N  n2      am1  0  0  -0.5600 1 1 8  1.0000 10.6800 CZ HH11 HH12 
+ARG_10:HH11         H  hn      am1  0  0   0.2800 0 0 8  1.0000  0.0000 NH1 
+ARG_10:HH12         H  hn      am1  0  0   0.2800 0 0 8  1.0000  0.0000 NH1 
+ARG_10:NH2          N  n2      am2  0  0  -0.5600 1 1 8  1.0000  9.4800 CZ HH21 HH22 
+ARG_10:HH21         H  hn      am2  0  0   0.2800 0 0 8  1.0000  0.0000 NH2 
+ARG_10:HH22         H  hn      am2  0  0   0.2800 0 0 8  1.0000  0.0000 NH2 
+SER_11:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.1900 CA ARG_10:C/1.5 HN 
+SER_11:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+SER_11:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.6000 C CB N HA 
+SER_11:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+SER_11:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.8400 O/2.0 CA ASN_12:N/1.5 
+SER_11:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.8400 C/2.0 
+SER_11:CB           C  c2      coh  0  0  -0.1700 0 0 8  1.0000  5.9100 OG CA HB1 HB2 
+SER_11:HB1          H  h       coh  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+SER_11:HB2          H  h       coh  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+SER_11:OG           O  oh      coh  0  0  -0.3800 1 0 8  1.0000  8.3800 CB HG 
+SER_11:HG           H  ho      coh  0  0   0.3500 0 0 8  1.0000  0.0000 OG 
+ASN_12:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.5400 CA SER_11:C/1.5 HN 
+ASN_12:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ASN_12:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.5700 C CB N HA 
+ASN_12:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ASN_12:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1400 O/2.0 CA PHE_13:N/1.5 
+ASN_12:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.5200 C/2.0 
+ASN_12:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  6.4200 CG CA HB1 HB2 
+ASN_12:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASN_12:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASN_12:CG           C  c'      coG  0  0   0.3800 1 1 8  1.0000  8.2500 OD1/2.0 ND2/1.5 CB 
+ASN_12:OD1          O  o'      coG  0  0  -0.3800 0 0 8  1.0000 12.7200 CG/2.0 
+ASN_12:ND2          N  n2      amD  0  0  -0.5600 1 1 8  1.0000  9.9200 CG/1.5 HD21 HD22 
+ASN_12:HD21         H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+ASN_12:HD22         H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+PHE_13:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.4300 CA ASN_12:C/1.5 HN 
+PHE_13:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+PHE_13:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.4900 C CB N HA 
+PHE_13:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PHE_13:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.4000 O/2.0 CA ASN_14:N/1.5 
+PHE_13:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.0700 C/2.0 
+PHE_13:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  5.4800 CG CA HB1 HB2 
+PHE_13:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PHE_13:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PHE_13:CG           C  cp      arG  0  0   0.0000 1 1 8  1.0000  5.5700 CD1/1.5 CD2/1.5 CB 
+PHE_13:CD1          C  cp      arD1 0  0  -0.1000 1 1 8  1.0000  6.9900 CE1/1.5 CG/1.5 HD1 
+PHE_13:HD1          H  h       arD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+PHE_13:CD2          C  cp      arD2 0  0  -0.1000 1 1 8  1.0000  6.5200 CG/1.5 CE2/1.5 HD2 
+PHE_13:HD2          H  h       arD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+PHE_13:CE1          C  cp      arE1 0  0  -0.1000 1 1 8  1.0000  8.2000 CZ/1.5 CD1/1.5 HE1 
+PHE_13:HE1          H  h       arE1 0  0   0.1000 0 0 8  1.0000  0.0000 CE1 
+PHE_13:CE2          C  cp      arE2 0  0  -0.1000 1 1 8  1.0000  6.3400 CD2/1.5 CZ/1.5 HE2 
+PHE_13:HE2          H  h       arE2 0  0   0.1000 0 0 8  1.0000  0.0000 CE2 
+PHE_13:CZ           C  cp      arZ  0  0  -0.1000 1 1 8  1.0000  6.8400 CE2/1.5 CE1/1.5 HZ 
+PHE_13:HZ           H  h       arZ  0  0   0.1000 0 0 8  1.0000  0.0000 CZ 
+ASN_14:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.6400 CA PHE_13:C/1.5 HN 
+ASN_14:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ASN_14:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.3100 C CB N HA 
+ASN_14:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ASN_14:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.9800 O/2.0 CA VAL_15:N/1.5 
+ASN_14:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.2200 C/2.0 
+ASN_14:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  5.8100 CG CA HB1 HB2 
+ASN_14:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASN_14:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASN_14:CG           C  c'      coG  0  0   0.3800 1 1 8  1.0000  6.8200 OD1/2.0 ND2/1.5 CB 
+ASN_14:OD1          O  o'      coG  0  0  -0.3800 0 0 8  1.0000  9.4300 CG/2.0 
+ASN_14:ND2          N  n2      amD  0  0  -0.5600 1 1 8  1.0000  8.2100 CG/1.5 HD21 HD22 
+ASN_14:HD21         H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+ASN_14:HD22         H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+VAL_15:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.7600 CA ASN_14:C/1.5 HN 
+VAL_15:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+VAL_15:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.9800 C CB N HA 
+VAL_15:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+VAL_15:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.8000 O/2.0 CA CYS_16:N/1.5 
+VAL_15:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.8500 C/2.0 
+VAL_15:CB           C  c1      meB  0  0  -0.1000 1 0 8  1.0000  4.7100 CG1 CG2 CA HB 
+VAL_15:HB           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+VAL_15:CG1          C  c3      meG1 0  0  -0.3000 1 0 8  1.0000  6.6700 CB HG11 HG12 HG13 
+VAL_15:HG11         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_15:HG12         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_15:HG13         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+VAL_15:CG2          C  c3      meG2 0  0  -0.3000 1 0 8  1.0000  6.2600 CB HG21 HG22 HG23 
+VAL_15:HG21         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+VAL_15:HG22         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+VAL_15:HG23         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+CYS_16:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.7900 CA VAL_15:C/1.5 HN 
+CYS_16:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_16:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.5400 C CB N HA 
+CYS_16:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_16:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.4800 O/2.0 CA ARG_17:N/1.5 
+CYS_16:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.6300 C/2.0 
+CYS_16:CB           C  c2      cs   0  0  -0.3000 1 0 8  1.0000  4.5800 SG CA HB1 HB2 
+CYS_16:HB1          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_16:HB2          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_16:SG           S  s1      cs   0  0   0.1000 0 0 8  1.0000  5.6600 CB CYS_26:SG 
+ARG_17:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.9900 CA CYS_16:C/1.5 HN 
+ARG_17:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ARG_17:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.8300 C CB N HA 
+ARG_17:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ARG_17:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.7900 O/2.0 CA LEU_18:N/1.5 
+ARG_17:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.3900 C/2.0 
+ARG_17:CB           C  c2      c3nc 0  0  -0.2000 0 0 8  1.0000  4.1100 CG CA HB1 HB2 
+ARG_17:HB1          H  h       c3nc 0  0   0.1100 0 0 8  1.0000  0.0000 CB 
+ARG_17:HB2          H  h       c3nc 0  0   0.1100 0 0 8  1.0000  0.0000 CB 
+ARG_17:CG           C  c2      c3nc 0  0  -0.2000 0 0 8  1.0000  4.6900 CD CB HG1 HG2 
+ARG_17:HG1          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CG 
+ARG_17:HG2          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CG 
+ARG_17:CD           C  c2      c3nc 0  0  -0.1600 1 0 8  1.0000  5.1000 NE CG HD1 HD2 
+ARG_17:HD1          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CD 
+ARG_17:HD2          H  h       c3nc 0  0   0.1300 0 0 8  1.0000  0.0000 CD 
+ARG_17:NE           N  n       c3nc 0  0  -0.5600 0 0 8  1.0000  4.7100 CZ/2.0 CD 
+ARG_17:CZ           C  cr      c3nc 0  0   0.3800 0 1 8  1.0000  5.2800 NH1 NH2 NE/2.0 
+ARG_17:NH1          N  n2      am1  0  0  -0.5600 1 1 8  1.0000  6.6700 CZ HH11 HH12 
+ARG_17:HH11         H  hn      am1  0  0   0.2800 0 0 8  1.0000  0.0000 NH1 
+ARG_17:HH12         H  hn      am1  0  0   0.2800 0 0 8  1.0000  0.0000 NH1 
+ARG_17:NH2          N  n2      am2  0  0  -0.5600 1 1 8  1.0000  6.4100 CZ HH21 HH22 
+ARG_17:HH21         H  hn      am2  0  0   0.2800 0 0 8  1.0000  0.0000 NH2 
+ARG_17:HH22         H  hn      am2  0  0   0.2800 0 0 8  1.0000  0.0000 NH2 
+LEU_18:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.7000 CA ARG_17:C/1.5 HN 
+LEU_18:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+LEU_18:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.4600 C CB N HA 
+LEU_18:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+LEU_18:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.1300 O/2.0 CA PRO_19:N/1.5 
+LEU_18:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.5500 C/2.0 
+LEU_18:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  6.4700 CG CA HB1 HB2 
+LEU_18:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+LEU_18:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+LEU_18:CG           C  c1      meG  0  0  -0.1000 1 0 8  1.0000  7.4300 CD1 CD2 CB HG 
+LEU_18:HG           H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+LEU_18:CD1          C  c3      meD1 0  0  -0.3000 1 0 8  1.0000  8.7000 CG HD11 HD12 HD13 
+LEU_18:HD11         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+LEU_18:HD12         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+LEU_18:HD13         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+LEU_18:CD2          C  c3      meD2 0  0  -0.3000 1 0 8  1.0000  9.3900 CG HD21 HD22 HD23 
+LEU_18:HD21         H  h       meD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+LEU_18:HD22         H  h       meD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+LEU_18:HD23         H  h       meD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+PRO_19:N            N  n       pepN 0  0  -0.4200 1 1 8  1.0000  4.2800 CA CD LEU_18:C/1.5 
+PRO_19:CA           C  ca      pepN 0  0   0.0600 0 0 8  1.0000  5.3800 C CB N HA 
+PRO_19:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PRO_19:CD           C  c2      pepN 0  0   0.0600 0 0 8  1.0000  6.4500 N CG HD1 HD2 
+PRO_19:HD1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_19:HD2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_19:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  6.3000 O/2.0 CA GLY_20:N/1.5 
+PRO_19:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.6200 C/2.0 
+PRO_19:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  5.8700 CG CA HB1 HB2 
+PRO_19:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_19:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_19:CG           C  c2      meG  0  0  -0.2000 1 0 8  1.0000  6.4700 CD CB HG1 HG2 
+PRO_19:HG1          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+PRO_19:HG2          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLY_20:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.9400 CA PRO_19:C/1.5 HN 
+GLY_20:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+GLY_20:CA           C  cg      pepN 0  0   0.0200 0 0 8  1.0000  5.3900 C N HA1 HA2 
+GLY_20:HA1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_20:HA2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_20:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.0300 O/2.0 CA THR_21:N/1.5 
+GLY_20:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.3400 C/2.0 
+THR_21:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.1000 CA GLY_20:C/1.5 HN 
+THR_21:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+THR_21:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  3.9400 C CB N HA 
+THR_21:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THR_21:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.9600 O/2.0 CA PRO_22:N/1.5 
+THR_21:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.8200 C/2.0 
+THR_21:CB           C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000  4.1300 CG2 OG1 CA HB 
+THR_21:HB           H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_21:OG1          O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000  5.4500 CB HG1 
+THR_21:HG1          H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THR_21:CG2          C  c3      meG  0  0  -0.3000 1 0 8  1.0000  5.4100 CB HG21 HG22 HG23 
+THR_21:HG21         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_21:HG22         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_21:HG23         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+PRO_22:N            N  n       pepN 0  0  -0.4200 1 1 8  1.0000  5.0400 CA CD THR_21:C/1.5 
+PRO_22:CA           C  ca      pepN 0  0   0.0600 0 0 8  1.0000  4.6900 C CB N HA 
+PRO_22:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PRO_22:CD           C  c2      pepN 0  0   0.0600 0 0 8  1.0000  4.9000 N CG HD1 HD2 
+PRO_22:HD1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_22:HD2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_22:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1900 O/2.0 CA GLU_23:N/1.5 
+PRO_22:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.4700 C/2.0 
+PRO_22:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  7.1200 CG CA HB1 HB2 
+PRO_22:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_22:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_22:CG           C  c2      meG  0  0  -0.2000 1 0 8  1.0000  7.0300 CD CB HG1 HG2 
+PRO_22:HG1          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+PRO_22:HG2          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLU_23:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.1600 CA PRO_22:C/1.5 HN 
+GLU_23:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+GLU_23:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.3100 C CB N HA 
+GLU_23:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLU_23:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1100 O/2.0 CA ALA_24:N/1.5 
+GLU_23:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.1100 C/2.0 
+GLU_23:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  6.1600 CG CA HB1 HB2 
+GLU_23:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+GLU_23:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+GLU_23:CG           C  c2      meG  0  0  -0.2000 1 0 8  1.0000  7.4800 CD CB HG1 HG2 
+GLU_23:HG1          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLU_23:HG2          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLU_23:CD           C  c'      cooh 0  0   0.3800 1 1 8  1.0000  9.4000 OE1/2.0 OE2 CG 
+GLU_23:OE1          O  o'      cooh 0  0  -0.3500 0 0 8  1.0000 10.4000 CD/2.0 
+GLU_23:OE2          O  oh      cooh 0  0  -0.3800 0 0 8  1.0000 13.3200 CD HE2 
+GLU_23:HE2          H  ho      cooh 0  0   0.3500 0 0 8  1.0000  0.0000 OE2 
+ALA_24:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.5600 CA GLU_23:C/1.5 HN 
+ALA_24:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ALA_24:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.4900 C CB N HA 
+ALA_24:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ALA_24:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1000 O/2.0 CA ILE_25:N/1.5 
+ALA_24:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.6400 C/2.0 
+ALA_24:CB           C  c3      meB  0  0  -0.3000 1 0 8  1.0000  5.8000 CA HB1 HB2 HB3 
+ALA_24:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_24:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_24:HB3          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_25:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.3700 CA ALA_24:C/1.5 HN 
+ILE_25:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ILE_25:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.4400 C CB N HA 
+ILE_25:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ILE_25:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.3200 O/2.0 CA CYS_26:N/1.5 
+ILE_25:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.7200 C/2.0 
+ILE_25:CB           C  c1      meB  0  0  -0.1000 1 0 8  1.0000  6.4200 CG2 CG1 CA HB 
+ILE_25:HB           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_25:CG1          C  c2      meG1 0  0  -0.2000 1 0 8  1.0000  7.5000 CD1 CB HG11 HG12 
+ILE_25:HG11         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_25:HG12         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_25:CG2          C  c3      meG2 0  0  -0.3000 1 0 8  1.0000  7.6500 CB HG21 HG22 HG23 
+ILE_25:HG21         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_25:HG22         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_25:HG23         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_25:CD1          C  c3      meD1 0  0  -0.3000 1 0 8  1.0000  7.8000 CG1 HD11 HD12 HD13 
+ILE_25:HD11         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_25:HD12         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_25:HD13         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+CYS_26:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.9200 CA ILE_25:C/1.5 HN 
+CYS_26:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_26:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.3700 C CB N HA 
+CYS_26:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_26:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  3.9500 O/2.0 CA ALA_27:N/1.5 
+CYS_26:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  4.7400 C/2.0 
+CYS_26:CB           C  c2      cs   0  0  -0.3000 1 0 8  1.0000  4.6300 SG CA HB1 HB2 
+CYS_26:HB1          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_26:HB2          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_26:SG           S  s1      cs   0  0   0.1000 0 0 8  1.0000  5.6100 CB CYS_16:SG 
+ALA_27:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  3.8900 CA CYS_26:C/1.5 HN 
+ALA_27:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ALA_27:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.4300 C CB N HA 
+ALA_27:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ALA_27:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.2600 O/2.0 CA THR_28:N/1.5 
+ALA_27:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.4400 C/2.0 
+ALA_27:CB           C  c3      meB  0  0  -0.3000 1 0 8  1.0000  5.3600 CA HB1 HB2 HB3 
+ALA_27:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_27:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_27:HB3          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_28:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.5300 CA ALA_27:C/1.5 HN 
+THR_28:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+THR_28:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.0800 C CB N HA 
+THR_28:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THR_28:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.6200 O/2.0 CA TYR_29:N/1.5 
+THR_28:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.8000 C/2.0 
+THR_28:CB           C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000  6.0300 CG2 OG1 CA HB 
+THR_28:HB           H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_28:OG1          O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000  7.1900 CB HG1 
+THR_28:HG1          H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THR_28:CG2          C  c3      meG  0  0  -0.3000 1 0 8  1.0000  7.3400 CB HG21 HG22 HG23 
+THR_28:HG21         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_28:HG22         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_28:HG23         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+TYR_29:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.0100 CA THR_28:C/1.5 HN 
+TYR_29:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+TYR_29:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  6.6000 C CB N HA 
+TYR_29:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+TYR_29:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.9200 O/2.0 CA THR_30:N/1.5 
+TYR_29:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.1300 C/2.0 
+TYR_29:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  9.6600 CG CA HB1 HB2 
+TYR_29:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+TYR_29:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+TYR_29:CG           C  cp      arG  0  0   0.0000 1 1 8  1.0000 11.5600 CD1/1.5 CD2/1.5 CB 
+TYR_29:CD1          C  cp      arD1 0  0  -0.1000 1 1 8  1.0000 12.8500 CE1/1.5 CG/1.5 HD1 
+TYR_29:HD1          H  h       arD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+TYR_29:CD2          C  cp      arD2 0  0  -0.1000 1 1 8  1.0000 14.4400 CG/1.5 CE2/1.5 HD2 
+TYR_29:HD2          H  h       arD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+TYR_29:CE1          C  cp      arE1 0  0  -0.1000 1 1 8  1.0000 16.6100 CZ/1.5 CD1/1.5 HE1 
+TYR_29:HE1          H  h       arE1 0  0   0.1000 0 0 8  1.0000  0.0000 CE1 
+TYR_29:CE2          C  cp      arE2 0  0  -0.1000 1 1 8  1.0000 17.1100 CD2/1.5 CZ/1.5 HE2 
+TYR_29:HE2          H  h       arE2 0  0   0.1000 0 0 8  1.0000  0.0000 CE2 
+TYR_29:CZ           C  cp      phol 0  0   0.0300 0 1 8  1.0000 19.9900 OH CE2/1.5 CE1/1.5 
+TYR_29:OH           O  oh      phol 0  0  -0.3800 1 0 8  1.0000 28.9800 CZ HH 
+TYR_29:HH           H  ho      phol 0  0   0.3500 0 0 8  1.0000  0.0000 OH 
+THR_30:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.3100 CA TYR_29:C/1.5 HN 
+THR_30:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+THR_30:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.7000 C CB N HA 
+THR_30:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THR_30:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  6.2800 O/2.0 CA GLY_31:N/1.5 
+THR_30:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  8.7700 C/2.0 
+THR_30:CB           C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000  6.5500 CG2 OG1 CA HB 
+THR_30:HB           H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_30:OG1          O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000  6.5700 CB HG1 
+THR_30:HG1          H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THR_30:CG2          C  c3      meG  0  0  -0.3000 1 0 8  1.0000  7.2900 CB HG21 HG22 HG23 
+THR_30:HG21         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_30:HG22         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_30:HG23         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+GLY_31:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.9900 CA THR_30:C/1.5 HN 
+GLY_31:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+GLY_31:CA           C  cg      pepN 0  0   0.0200 0 0 8  1.0000  5.5000 C N HA1 HA2 
+GLY_31:HA1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_31:HA2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_31:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.1900 O/2.0 CA CYS_32:N/1.5 
+GLY_31:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.1200 C/2.0 
+CYS_32:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.3000 CA GLY_31:C/1.5 HN 
+CYS_32:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_32:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  4.8900 C CB N HA 
+CYS_32:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_32:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.5000 O/2.0 CA ILE_33:N/1.5 
+CYS_32:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  5.8200 C/2.0 
+CYS_32:CB           C  c2      cs   0  0  -0.3000 1 0 8  1.0000  4.6600 SG CA HB1 HB2 
+CYS_32:HB1          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_32:HB2          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_32:SG           S  s1      cs   0  0   0.1000 0 0 8  1.0000  5.3300 CB CYS_4:SG 
+ILE_33:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  6.0200 CA CYS_32:C/1.5 HN 
+ILE_33:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ILE_33:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.2400 C CB N HA 
+ILE_33:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ILE_33:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.1600 O/2.0 CA ILE_34:N/1.5 
+ILE_33:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.1900 C/2.0 
+ILE_33:CB           C  c1      meB  0  0  -0.1000 1 0 8  1.0000  5.4900 CG2 CG1 CA HB 
+ILE_33:HB           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_33:CG1          C  c2      meG1 0  0  -0.2000 1 0 8  1.0000  6.8500 CD1 CB HG11 HG12 
+ILE_33:HG11         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_33:HG12         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_33:CG2          C  c3      meG2 0  0  -0.3000 1 0 8  1.0000  6.4500 CB HG21 HG22 HG23 
+ILE_33:HG21         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_33:HG22         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_33:HG23         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_33:CD1          C  c3      meD1 0  0  -0.3000 1 0 8  1.0000  8.9400 CG1 HD11 HD12 HD13 
+ILE_33:HD11         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_33:HD12         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_33:HD13         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_34:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.5200 CA ILE_33:C/1.5 HN 
+ILE_34:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ILE_34:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  6.8200 C CB N HA 
+ILE_34:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ILE_34:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  6.9200 O/2.0 CA ILE_35:N/1.5 
+ILE_34:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.2200 C/2.0 
+ILE_34:CB           C  c1      meB  0  0  -0.1000 1 0 8  1.0000  8.1100 CG2 CG1 CA HB 
+ILE_34:HB           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_34:CG1          C  c2      meG1 0  0  -0.2000 1 0 8  1.0000  9.5900 CD1 CB HG11 HG12 
+ILE_34:HG11         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_34:HG12         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_34:CG2          C  c3      meG2 0  0  -0.3000 1 0 8  1.0000  9.7300 CB HG21 HG22 HG23 
+ILE_34:HG21         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_34:HG22         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_34:HG23         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_34:CD1          C  c3      meD1 0  0  -0.3000 1 0 8  1.0000 13.4100 CG1 HD11 HD12 HD13 
+ILE_34:HD11         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_34:HD12         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_34:HD13         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_35:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  7.0600 CA ILE_34:C/1.5 HN 
+ILE_35:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ILE_35:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  7.5200 C CB N HA 
+ILE_35:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ILE_35:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  6.6300 O/2.0 CA PRO_36:N/1.5 
+ILE_35:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.9000 C/2.0 
+ILE_35:CB           C  c1      meB  0  0  -0.1000 1 0 8  1.0000  8.0700 CG2 CG1 CA HB 
+ILE_35:HB           H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ILE_35:CG1          C  c2      meG1 0  0  -0.2000 1 0 8  1.0000  9.4100 CD1 CB HG11 HG12 
+ILE_35:HG11         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_35:HG12         H  h       meG1 0  0   0.1000 0 0 8  1.0000  0.0000 CG1 
+ILE_35:CG2          C  c3      meG2 0  0  -0.3000 1 0 8  1.0000  9.4600 CB HG21 HG22 HG23 
+ILE_35:HG21         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_35:HG22         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_35:HG23         H  h       meG2 0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+ILE_35:CD1          C  c3      meD1 0  0  -0.3000 1 0 8  1.0000  9.8500 CG1 HD11 HD12 HD13 
+ILE_35:HD11         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_35:HD12         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+ILE_35:HD13         H  h       meD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+PRO_36:N            N  n       pepN 0  0  -0.4200 1 1 8  1.0000  8.0700 CA CD ILE_35:C/1.5 
+PRO_36:CA           C  ca      pepN 0  0   0.0600 0 0 8  1.0000  8.7800 C CB N HA 
+PRO_36:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PRO_36:CD           C  c2      pepN 0  0   0.0600 0 0 8  1.0000  9.5300 N CG HD1 HD2 
+PRO_36:HD1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_36:HD2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_36:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  8.3100 O/2.0 CA GLY_37:N/1.5 
+PRO_36:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.0900 C/2.0 
+PRO_36:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  9.6700 CG CA HB1 HB2 
+PRO_36:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_36:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_36:CG           C  c2      meG  0  0  -0.2000 1 0 8  1.0000 10.1500 CD CB HG1 HG2 
+PRO_36:HG1          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+PRO_36:HG2          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLY_37:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  8.4800 CA PRO_36:C/1.5 HN 
+GLY_37:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+GLY_37:CA           C  cg      pepN 0  0   0.0200 0 0 8  1.0000  9.2000 C N HA1 HA2 
+GLY_37:HA1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_37:HA2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_37:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000 10.4100 O/2.0 CA ALA_38:N/1.5 
+GLY_37:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000 12.0600 C/2.0 
+ALA_38:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  9.2400 CA GLY_37:C/1.5 HN 
+ALA_38:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ALA_38:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  9.2400 C CB N HA 
+ALA_38:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ALA_38:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  9.6000 O/2.0 CA THR_39:N/1.5 
+ALA_38:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000 13.6500 C/2.0 
+ALA_38:CB           C  c3      meB  0  0  -0.3000 1 0 8  1.0000 10.4300 CA HB1 HB2 HB3 
+ALA_38:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_38:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_38:HB3          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_39:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  8.7000 CA ALA_38:C/1.5 HN 
+THR_39:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+THR_39:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  9.4600 C CB N HA 
+THR_39:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+THR_39:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  8.3200 O/2.0 CA CYS_40:N/1.5 
+THR_39:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.8900 C/2.0 
+THR_39:CB           C  c1      cBoh 0  0  -0.0700 0 0 8  1.0000 10.7200 CG2 OG1 CA HB 
+THR_39:HB           H  h       cBoh 0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+THR_39:OG1          O  oh      cBoh 0  0  -0.3800 1 0 8  1.0000 11.6600 CB HG1 
+THR_39:HG1          H  ho      cBoh 0  0   0.3500 0 0 8  1.0000  0.0000 OG1 
+THR_39:CG2          C  c3      meG  0  0  -0.3000 1 0 8  1.0000 11.8100 CB HG21 HG22 HG23 
+THR_39:HG21         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_39:HG22         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+THR_39:HG23         H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG2 
+CYS_40:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  7.6400 CA THR_39:C/1.5 HN 
+CYS_40:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+CYS_40:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  8.0500 C CB N HA 
+CYS_40:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+CYS_40:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  7.6300 O/2.0 CA PRO_41:N/1.5 
+CYS_40:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  9.6400 C/2.0 
+CYS_40:CB           C  c2      cs   0  0  -0.3000 1 0 8  1.0000  7.8000 SG CA HB1 HB2 
+CYS_40:HB1          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_40:HB2          H  h       cs   0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+CYS_40:SG           S  s1      cs   0  0   0.1000 0 0 8  1.0000  7.3000 CB CYS_3:SG 
+PRO_41:N            N  n       pepN 0  0  -0.4200 1 1 8  1.0000  8.0000 CA CD CYS_40:C/1.5 
+PRO_41:CA           C  ca      pepN 0  0   0.0600 0 0 8  1.0000  8.9600 C CB N HA 
+PRO_41:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+PRO_41:CD           C  c2      pepN 0  0   0.0600 0 0 8  1.0000 10.4900 N CG HD1 HD2 
+PRO_41:HD1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_41:HD2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CD 
+PRO_41:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  9.0600 O/2.0 CA GLY_42:N/1.5 
+PRO_41:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  8.8200 C/2.0 
+PRO_41:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000 10.3900 CG CA HB1 HB2 
+PRO_41:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_41:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+PRO_41:CG           C  c2      meG  0  0  -0.2000 1 0 8  1.0000 10.9900 CD CB HG1 HG2 
+PRO_41:HG1          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+PRO_41:HG2          H  h       meG  0  0   0.1000 0 0 8  1.0000  0.0000 CG 
+GLY_42:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  7.5500 CA PRO_41:C/1.5 HN 
+GLY_42:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+GLY_42:CA           C  cg      pepN 0  0   0.0200 0 0 8  1.0000  8.0000 C N HA1 HA2 
+GLY_42:HA1          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_42:HA2          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+GLY_42:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  7.2200 O/2.0 CA ASP_43:N/1.5 
+GLY_42:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  8.4100 C/2.0 
+ASP_43:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.5400 CA GLY_42:C/1.5 HN 
+ASP_43:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ASP_43:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.8500 C CB N HA 
+ASP_43:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ASP_43:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  5.8700 O/2.0 CA TYR_44:N/1.5 
+ASP_43:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.2900 C/2.0 
+ASP_43:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  6.7200 CG CA HB1 HB2 
+ASP_43:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASP_43:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASP_43:CG           C  c'      cooh 0  0   0.3800 1 1 8  1.0000  8.5900 OD1/2.0 OD2 CB 
+ASP_43:OD1          O  o'      cooh 0  0  -0.3500 0 0 8  1.0000  9.5900 CG/2.0 
+ASP_43:OD2          O  oh      cooh 0  0  -0.3800 0 0 8  1.0000 11.4500 CG HD2 
+ASP_43:HD2          H  ho      cooh 0  0   0.3500 0 0 8  1.0000  0.0000 OD2 
+TYR_44:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.2200 CA ASP_43:C/1.5 HN 
+TYR_44:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+TYR_44:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.5600 C CB N HA 
+TYR_44:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+TYR_44:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  4.6100 O/2.0 CA ALA_45:N/1.5 
+TYR_44:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  6.0400 C/2.0 
+TYR_44:CB           C  c2      meB  0  0  -0.2000 1 0 8  1.0000  5.4100 CG CA HB1 HB2 
+TYR_44:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+TYR_44:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+TYR_44:CG           C  cp      arG  0  0   0.0000 1 1 8  1.0000  5.3400 CD1/1.5 CD2/1.5 CB 
+TYR_44:CD1          C  cp      arD1 0  0  -0.1000 1 1 8  1.0000  6.5900 CE1/1.5 CG/1.5 HD1 
+TYR_44:HD1          H  h       arD1 0  0   0.1000 0 0 8  1.0000  0.0000 CD1 
+TYR_44:CD2          C  cp      arD2 0  0  -0.1000 1 1 8  1.0000  5.9400 CG/1.5 CE2/1.5 HD2 
+TYR_44:HD2          H  h       arD2 0  0   0.1000 0 0 8  1.0000  0.0000 CD2 
+TYR_44:CE1          C  cp      arE1 0  0  -0.1000 1 1 8  1.0000  5.9700 CZ/1.5 CD1/1.5 HE1 
+TYR_44:HE1          H  h       arE1 0  0   0.1000 0 0 8  1.0000  0.0000 CE1 
+TYR_44:CE2          C  cp      arE2 0  0  -0.1000 1 1 8  1.0000  5.1700 CD2/1.5 CZ/1.5 HE2 
+TYR_44:HE2          H  h       arE2 0  0   0.1000 0 0 8  1.0000  0.0000 CE2 
+TYR_44:CZ           C  cp      phol 0  0   0.0300 0 1 8  1.0000  5.9600 OH CE2/1.5 CE1/1.5 
+TYR_44:OH           O  oh      phol 0  0  -0.3800 1 0 8  1.0000  8.6000 CZ HH 
+TYR_44:HH           H  ho      phol 0  0   0.3500 0 0 8  1.0000  0.0000 OH 
+ALA_45:N            N  n       pepN 0  0  -0.5000 1 1 8  1.0000  4.7600 CA TYR_44:C/1.5 HN 
+ALA_45:HN           H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ALA_45:CA           C  ca      pepN 0  0   0.1200 0 0 8  1.0000  5.8900 C CB N HA 
+ALA_45:HA           H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ALA_45:C            C  c'      pepC 0  0   0.3800 1 1 8  1.0000  6.6700 O/2.0 CA ASNC_46:N/1.5 
+ALA_45:O            O  o'      pepC 0  0  -0.3800 0 0 8  1.0000  7.5600 C/2.0 
+ALA_45:CB           C  c3      meB  0  0  -0.3000 1 0 8  1.0000  6.8200 CA HB1 HB2 HB3 
+ALA_45:HB1          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_45:HB2          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ALA_45:HB3          H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASNC_46:N           N  n       pepN 0  0  -0.5000 1 1 8  1.0000  5.8000 CA ALA_45:C/1.5 HN 
+ASNC_46:HN          H  hn      pepN 0  0   0.2800 0 0 8  1.0000  0.0000 N 
+ASNC_46:CA          C  ca      pepN 0  0   0.1200 0 0 8  1.0000  6.1500 C CB N HA 
+ASNC_46:HA          H  h       pepN 0  0   0.1000 0 0 8  1.0000  0.0000 CA 
+ASNC_46:C           C  c-      pep- 0  0   0.1400 1 1 8  1.0000  6.6100 O/1.5 OXT/1.5 CA 
+ASNC_46:O           O  o-      pep- 0  0  -0.5700 0 0 8  1.0000  7.1800 C/1.5 
+ASNC_46:OXT         O  o-      pep- 0  0  -0.5700 0 0 8  1.0000  7.8600 C/1.5 
+ASNC_46:CB          C  c2      meB  0  0  -0.2000 1 0 8  1.0000  7.2700 CG CA HB1 HB2 
+ASNC_46:HB1         H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASNC_46:HB2         H  h       meB  0  0   0.1000 0 0 8  1.0000  0.0000 CB 
+ASNC_46:CG          C  c'      coG  0  0   0.3800 1 1 8  1.0000  7.9800 OD1/2.0 ND2/1.5 CB 
+ASNC_46:OD1         O  o'      coG  0  0  -0.3800 0 0 8  1.0000 11.0000 CG/2.0 
+ASNC_46:ND2         N  n2      amD  0  0  -0.5600 1 1 8  1.0000 10.3200 CG/1.5 HD21 HD22 
+ASNC_46:HD21        H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+ASNC_46:HD22        H  hn      amD  0  0   0.2800 0 0 8  1.0000  0.0000 ND2 
+
+
+#atomset                                                                      
+
+
+@quartet torsion *:*_*:chi1
+N      CA     CB     OG1   
+
+@quartet torsion *:*_*:chi2
+CA     CB     OG1    HG1   
+
+@quartet torsion *:*_*:ch2'
+CA     CB     CG2    HG21  
+
+@quartet torsion *:*_*:psi 
+N      CA     C      *:N   
+
+@quartet torsion *:*_*:omeg
+CA     C      *:N    *:CA  
+
+@quartet torsion *:*_*:phi 
+*:C    N      CA     C     
+
+@quartet torsion *:CYS_*:chi1
+N      CA     CB     SG    
+
+@quartet torsion *:*_*:chi1
+N      CA     CB     CG    
+
+@quartet torsion *:SER_*:chi1
+N      CA     CB     OG    
+
+@quartet torsion *:SER_*:chi2
+CA     CB     OG     HG    
+
+@quartet torsion *:*_*:chi1
+N      CA     CB     CG1   
+
+@quartet torsion *:ILE_*:chi2
+CA     CB     CG1    CD1   
+
+@quartet torsion *:ILE_*:chi3
+CB     CG1    CD1    HD11  
+
+@quartet torsion *:VAL_*:chi2
+CA     CB     CG1    HG11  
+
+@quartet torsion *:ALA_*:chi1
+N      CA     CB     HB1   
+
+@quartet torsion *:*_*:chi2
+CA     CB     CG     CD    
+
+@quartet torsion *:ARG_*:chi3
+CB     CG     CD     NE    
+
+@quartet torsion *:ARG_*:chi4
+CG     CD     NE     CZ    
+
+@quartet torsion *:ARG_*:chi5
+CD     NE     CZ     NH1   
+
+@quartet torsion *:*_*:chi2
+CA     CB     CG     ND2   
+
+@quartet torsion *:*_*:chi3
+CB     CG     ND2    HD21  
+
+@quartet torsion *:*_*:chi2
+CA     CB     CG     CD1   
+
+@quartet torsion *:LEU_18:chi3
+CB     CG     CD1    HD11  
+
+@quartet torsion *:LEU_18:ch2'
+CA     CB     CG     CD2   
+
+@quartet torsion *:LEU_18:ch3'
+CB     CG     CD2    HD21  
+
+@quartet torsion *:GLU_23:chi3
+CB     CG     CD     OE2   
+
+@quartet torsion *:GLU_23:chi4
+CG     CD     OE2    HE2   
+
+@quartet torsion *:TYR_*:chi3
+CE1    CZ     OH     HH    
+
+@quartet torsion *:ASP_43:chi2
+CA     CB     CG     OD2   
+
+@quartet torsion *:ASP_43:chi3
+CB     CG     OD2    HD2   
+
+
+@list subset  CRN$TURNT1
+CRAMBIN:PRO_41:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2 
+GLY_42:N HN CA HA1 HA2 C O 
+ASP_43:N HN CA HA C O CB HB1 HB2 CG OD1 OD2 HD2 
+TYR_44:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH 
+
+@list subset  CRN$TURN
+CRAMBIN:PRO_41:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2 
+GLY_42:N HN CA HA1 HA2 C O 
+ASP_43:N HN CA HA C O CB HB1 HB2 CG OD1 OD2 HD2 
+TYR_44:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH 
+
+@list subset  CRN$SHEETS1
+CRAMBIN:THRN_1:N HN3 HN1 HN2 CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+THR_2:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+CYS_3:N HN CA HA C O CB HB1 HB2 SG 
+CYS_4:N HN CA HA C O CB HB1 HB2 SG 
+CYS_32:N HN CA HA C O CB HB1 HB2 SG 
+ILE_33:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+ILE_34:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+ILE_35:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+
+@list subset  CRN$SHEET
+CRAMBIN:THRN_1:N HN3 HN1 HN2 CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+THR_2:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+CYS_3:N HN CA HA C O CB HB1 HB2 SG 
+CYS_4:N HN CA HA C O CB HB1 HB2 SG 
+CYS_32:N HN CA HA C O CB HB1 HB2 SG 
+ILE_33:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+ILE_34:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+ILE_35:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+
+@list subset  CRN$HELIXH2
+CRAMBIN:GLU_23:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD OE1 OE2 HE2 
+ALA_24:N HN CA HA C O CB HB1 HB2 HB3 
+ILE_25:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+CYS_26:N HN CA HA C O CB HB1 HB2 SG 
+ALA_27:N HN CA HA C O CB HB1 HB2 HB3 
+THR_28:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+TYR_29:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH 
+THR_30:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+
+@list subset  CRN$HELIXH1
+CRAMBIN:ILE_7:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+VAL_8:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23 
+ALA_9:N HN CA HA C O CB HB1 HB2 HB3 
+ARG_10:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22 
+SER_11:N HN CA HA C O CB HB1 HB2 OG HG 
+ASN_12:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22 
+PHE_13:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ 
+ASN_14:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22 
+VAL_15:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23 
+CYS_16:N HN CA HA C O CB HB1 HB2 SG 
+ARG_17:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22 
+LEU_18:N HN CA HA C O CB HB1 HB2 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23 
+PRO_19:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2 
+
+@list subset  CRN$HELIX
+CRAMBIN:ILE_7:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+VAL_8:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23 
+ALA_9:N HN CA HA C O CB HB1 HB2 HB3 
+ARG_10:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22 
+SER_11:N HN CA HA C O CB HB1 HB2 OG HG 
+ASN_12:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22 
+PHE_13:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ 
+ASN_14:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22 
+VAL_15:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23 
+CYS_16:N HN CA HA C O CB HB1 HB2 SG 
+ARG_17:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22 
+LEU_18:N HN CA HA C O CB HB1 HB2 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23 
+PRO_19:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2 
+GLU_23:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD OE1 OE2 HE2 
+ALA_24:N HN CA HA C O CB HB1 HB2 HB3 
+ILE_25:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13 
+CYS_26:N HN CA HA C O CB HB1 HB2 SG 
+ALA_27:N HN CA HA C O CB HB1 HB2 HB3 
+THR_28:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+TYR_29:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH 
+THR_30:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23 
+#end
+

tools/msi2lmp/test/nylon.car

@@ -0,0 +1,124 @@
+!BIOSYM archive 3                                                               
+PBC=OFF                                                                         
+input file for discover                                                         
+!DATE Mon Jul 14 17:01:24 1997                                                  
+C        1.493000031   20.593999863   -0.449999988 MOL  1      c2      C   0.220
+C1       2.328000069   19.871000290    0.623000026 MOL  1      c2      C  -0.200
+C2       2.887000084   20.902999878    1.621000051 MOL  1      c2      C  -0.200
+C3       3.533999920   20.169000626    2.809999943 MOL  1      c2      C  -0.200
+C4       4.085000038   21.201000214    3.812999964 MOL  1      c2      C  -0.200
+C5       4.731999874   20.466999054    5.001999855 MOL  1      c2      C   0.020
+N        5.270999908   21.479000092    5.985000134 MOL  1      n       N  -0.500
+C6       6.477000237   21.142000198    6.829999924 MOL  1      c'      C   0.380
+O        7.435999870   22.232000351    7.244999886 MOL  1      o'      O  -0.380
+C7       6.728000164   19.687000275    7.267000198 MOL  1      c2      C  -0.200
+C8       7.763999939   19.665000916    8.406999588 MOL  1      c2      C  -0.200
+C9       7.464000225   18.486000061    9.350999832 MOL  1      c2      C  -0.200
+C10      8.416000366   18.541000366   10.560999870 MOL  1      c2      C  -0.200
+C11      8.112999916   17.364999771   11.506999969 MOL  1      c'      C   0.380
+O1       6.711999893   16.809000015   11.597000122 MOL  1      o'      O  -0.380
+HC1      2.111000061   20.704999924   -1.401000023 MOL  1      h       H   0.100
+HC2      1.195999980   21.625999451   -0.067000002 MOL  1      h       H   0.100
+H11      3.191999912   19.319000244    0.125000000 MOL  1      h       H   0.100
+H12      1.669999957   19.124000549    1.179000020 MOL  1      h       H   0.100
+H21      3.670000076   21.548999786    1.101999998 MOL  1      h       H   0.100
+H22      2.039000034   21.563999176    1.998999953 MOL  1      h       H   0.100
+H31      4.388000011   19.513999939    2.434000015 MOL  1      h       H   0.100
+H32      2.753999949   19.517999649    3.325999975 MOL  1      h       H   0.100
+H41      4.866000175   21.853000641    3.298000097 MOL  1      h       H   0.100
+H42      3.232000113   21.857000351    4.190000057 MOL  1      h       H   0.100
+H51      5.585000038   19.811000824    4.625999928 MOL  1      h       H   0.100
+H52      3.951999903   19.815999985    5.518000126 MOL  1      h       H   0.100
+HN       4.782000065   22.469999313    6.085999966 MOL  1      hn      H   0.280
+H71      7.124000072   19.086999893    6.382999897 MOL  1      h       H   0.100
+H72      5.751999855   19.225000381    7.632999897 MOL  1      h       H   0.100
+H81      8.809000015   19.542999268    7.967999935 MOL  1      h       H   0.100
+H82      7.709000111   20.642000198    8.989999771 MOL  1      h       H   0.100
+H91      7.614999771   17.503000259    8.793999672 MOL  1      h       H   0.100
+H92      6.385000229   18.555000305    9.713999748 MOL  1      h       H   0.100
+H101     9.494999886   18.468999863   10.199000359 MOL  1      h       H   0.100
+H102     8.267000198   19.524000168   11.118000031 MOL  1      h       H   0.100
+N1       9.217000008   16.766000748   12.345000267 MOL  1      n       N  -0.500
+C12      8.902999878   16.179000854   13.701000214 MOL  1      c2      C   0.020
+C13      9.892000198   15.039999962   14.008999825 MOL  1      c2      C  -0.200
+C14      9.138999939   13.871000290   14.671999931 MOL  1      c2      C  -0.200
+C15     10.074000359   12.652999878   14.779999733 MOL  1      c2      C  -0.200
+C16      9.317999840   11.480999947   15.434000015 MOL  1      c2      C  -0.200
+C17     10.253000259   10.262000084   15.543000221 MOL  1      c2      C   0.020
+N2       9.512000084    9.114000320   16.184000015 MOL  1      n       N  -0.500
+C18     10.263999939    8.095999718   17.007999420 MOL  1      c'      C   0.380
+O2      11.720000267    8.319999695   17.337999344 MOL  1      o'      O  -0.380
+C19      9.545000076    6.831999779   17.513000488 MOL  1      c2      C  -0.200
+C20     10.385999680    6.170000076   18.621000290 MOL  1      c2      C  -0.200
+C21      9.451999664    5.482999802   19.634000778 MOL  1      c2      C  -0.200
+C22     10.281999588    4.934999943   20.809999466 MOL  1      c2      C  -0.200
+H221    10.808575630    5.755126953   21.298067093 MOL  1      h       H   0.100
+H222    11.006152153    4.209916592   20.438573837 MOL  1      h       H   0.100
+C23      9.347999573    4.250999928   21.825000763 MOL  1      c'      C   0.380
+O3       9.854000092    3.098999977   22.659999847 MOL  1      o'      O  -0.380
+H1      10.260000229   16.757999420   11.965000153 MOL  1      hn      H   0.280
+H121     8.998000145   16.989000320   14.496999741 MOL  1      h       H   0.100
+H122     7.839000225   15.769000053   13.699999809 MOL  1      h       H   0.100
+H131    10.701999664   15.418999672   14.715999603 MOL  1      h       H   0.100
+H132    10.373000145   14.680000305   13.039999962 MOL  1      h       H   0.100
+H141     8.796999931   14.180999756   15.713999748 MOL  1      h       H   0.100
+H142     8.229999542   13.597000122   14.039999962 MOL  1      h       H   0.100
+H151    10.979000092   12.923000336   15.418000221 MOL  1      h       H   0.100
+H152    10.421999931   12.345999718   13.739000320 MOL  1      h       H   0.100
+H161     8.970999718   11.786999702   16.475999832 MOL  1      h       H   0.100
+H162     8.413000107   11.208999634   14.796999931 MOL  1      h       H   0.100
+H171    11.159000397   10.532999992   16.180000305 MOL  1      h       H   0.100
+H172    10.600999832    9.956000328   14.501000404 MOL  1      h       H   0.100
+H2       8.413999557    9.017000198   16.048999786 MOL  1      hn      H   0.280
+H191     9.411000252    6.098999977   16.649999619 MOL  1      h       H   0.100
+H192     8.522999763    7.116000175   17.930999756 MOL  1      h       H   0.100
+H201    11.081000328    5.394000053   18.159000397 MOL  1      h       H   0.100
+H202    11.005000114    6.965000153   19.155000687 MOL  1      h       H   0.100
+H211     8.904000282    4.623000145   19.124000549 MOL  1      h       H   0.100
+H212     8.692000389    6.237999916   20.024999619 MOL  1      h       H   0.100
+N3       7.925000191    4.731999874   21.985000610 MOL  1      n       N  -0.500
+C24      7.053999901    4.160999775   23.077999115 MOL  1      c2      C   0.020
+C25      6.034999847    5.223000050   23.531999588 MOL  1      c2      C  -0.200
+C26      5.895999908    5.179999828   25.065000534 MOL  1      c2      C  -0.200
+C27      5.052000046    6.377999783   25.538000107 MOL  1      c2      C  -0.200
+C28      4.921000004    6.340000153   27.072000504 MOL  1      c2      C  -0.200
+C29      4.077000141    7.538000107   27.545999527 MOL  1      c2      C   0.020
+N4       3.948999882    7.500999928   29.049999237 MOL  1      n       N  -0.500
+C30      2.717999935    8.065999985   29.716999054 MOL  1      c'      C   0.380
+O4       1.600000024    8.638999939   28.878000259 MOL  1      o'      O  -0.380
+C31      2.601000071    8.059000015   31.252000809 MOL  1      c2      C  -0.200
+C32      1.139000058    8.319000244   31.658000946 MOL  1      c2      C  -0.200
+C33      0.828000009    7.570000172   32.967998505 MOL  1      c2      C  -0.200
+C34     -0.667999983    7.721000195   33.304000854 MOL  1      c2      C  -0.200
+C35     -0.978999972    6.969999790   34.611000061 MOL  1      c'      C   0.450
+O5      -2.085999966    7.455999851   35.515998840 MOL  1      o-      O  -0.500
+H3       7.519999981    5.506000042   21.299999237 MOL  1      hn      H   0.280
+H241     6.498000145    3.246999979   22.683000565 MOL  1      h       H   0.100
+H242     7.703999996    3.855999947   23.962999344 MOL  1      h       H   0.100
+H251     5.022999763    5.008999825   23.052999496 MOL  1      h       H   0.100
+H252     6.395999908    6.256000042   23.211999893 MOL  1      h       H   0.100
+H261     5.383999825    4.209000111   25.372999191 MOL  1      h       H   0.100
+H262     6.929999828    5.231999874   25.541999817 MOL  1      h       H   0.100
+H271     4.014999866    6.322000027   25.068000793 MOL  1      h       H   0.100
+H272     5.559999943    7.348999977   25.224000931 MOL  1      h       H   0.100
+H281     4.413000107    5.369999886   27.386999130 MOL  1      h       H   0.100
+H282     5.958000183    6.395999908   27.544000626 MOL  1      h       H   0.100
+H291     3.039999962    7.482999802   27.075000763 MOL  1      h       H   0.100
+H292     4.585000038    8.508999825   27.232000351 MOL  1      h       H   0.100
+H4       4.760000229    7.059000015   29.665000916 MOL  1      hn      H   0.280
+H311     3.266999960    8.875000000   31.687999725 MOL  1      h       H   0.100
+H312     2.931999922    7.044000149   31.653999329 MOL  1      h       H   0.100
+H321     0.980000019    9.437000275   31.813999176 MOL  1      h       H   0.100
+H322     0.442999989    7.947999954   30.834999084 MOL  1      h       H   0.100
+H331     1.452999949    8.008000374   33.813999176 MOL  1      h       H   0.100
+H332     1.078999996    6.465000153   32.842998505 MOL  1      h       H   0.100
+H341    -0.919000030    8.826000214   33.431999207 MOL  1      h       H   0.100
+H342    -1.294000030    7.285999775   32.457000732 MOL  1      h       H   0.100
+O6      -0.179000005    5.745999813   34.987998962 MOL  1      o-      O  -0.500
+N5       0.250000000   19.790000916   -0.746999979 MOL  1      n4      N  -0.500
+HN51     0.118000001   19.704999924   -1.845999956 MOL  1      hn      H   0.360
+HN52    -0.634000003   20.298000336   -0.307000011 MOL  1      hn      H   0.360
+H53      0.349999994   18.775999069   -0.307000011 MOL  1      hn      H   0.360
+end                                                                             
+end                                                                             
+

tools/msi2lmp/test/nylon.mdf

@@ -0,0 +1,142 @@
+!BIOSYM molecular_data 4
+
+!DATE:      Mon Jul 14 17:01:24 1997     INSIGHT generated molecular data file 
+
+#topology                                                                      
+
+@column 1 element                                                              
+@column 2 atom_type cvff                                                       
+@column 3 charge_group cvff                                                    
+@column 4 isotope                                                              
+@column 5 formal_charge                                                        
+@column 6 charge cvff                                                          
+@column 7 switching_atom cvff                                                  
+@column 8 oop_flag cvff                                                        
+@column 9 chirality_flag                                                       
+@column 10 occupancy                                                           
+@column 11 xray_temp_factor                                                    
+@column 12 connections                                                         
+
+@molecule NYLON2                                                              
+
+MOL_1:C             C  c2      MOL  0  0   0.2200 0 0 8  1.0000  0.0000 C1 HC1 HC2 N5 
+MOL_1:C1            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C C2 H11 H12 
+MOL_1:C2            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C1 C3 H21 H22 
+MOL_1:C3            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C2 C4 H31 H32 
+MOL_1:C4            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C3 C5 H41 H42 
+MOL_1:C5            C  c2      MOL  0  0   0.0200 0 0 8  1.0000  0.0000 C4 N H51 H52 
+MOL_1:N             N  n       MOL  0  0  -0.5000 0 1 8  1.0000  0.0000 C5 C6 HN 
+MOL_1:C6            C  c'      MOL  0  0   0.3800 0 1 8  1.0000  0.0000 N O/2.0 C7 
+MOL_1:O             O  o'      MOL  0  0  -0.3800 0 0 8  1.0000  0.0000 C6/2.0 
+MOL_1:C7            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C6 C8 H71 H72 
+MOL_1:C8            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C7 C9 H81 H82 
+MOL_1:C9            C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C8 C10 H91 H92 
+MOL_1:C10           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C9 C11 H101 H102 
+MOL_1:C11           C  c'      MOL  0  0   0.3800 0 1 8  1.0000  0.0000 C10 O1/2.0 N1/1.5 
+MOL_1:O1            O  o'      MOL  0  0  -0.3800 0 0 8  1.0000  0.0000 C11/2.0 
+MOL_1:HC1           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C 
+MOL_1:HC2           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C 
+MOL_1:H11           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C1 
+MOL_1:H12           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C1 
+MOL_1:H21           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C2 
+MOL_1:H22           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C2 
+MOL_1:H31           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C3 
+MOL_1:H32           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C3 
+MOL_1:H41           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C4 
+MOL_1:H42           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C4 
+MOL_1:H51           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C5 
+MOL_1:H52           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C5 
+MOL_1:HN            H  hn      MOL  0  0   0.2800 0 0 8  1.0000  0.0000 N 
+MOL_1:H71           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C7 
+MOL_1:H72           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C7 
+MOL_1:H81           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C8 
+MOL_1:H82           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C8 
+MOL_1:H91           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C9 
+MOL_1:H92           H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C9 
+MOL_1:H101          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C10 
+MOL_1:H102          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C10 
+MOL_1:N1            N  n       MOL  0  0  -0.5000 0 1 8  1.0000  0.0000 C11/1.5 C12 H1 
+MOL_1:C12           C  c2      MOL  0  0   0.0200 0 0 8  1.0000  0.0000 N1 C13 H121 H122 
+MOL_1:C13           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C12 C14 H131 H132 
+MOL_1:C14           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C13 C15 H141 H142 
+MOL_1:C15           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C14 C16 H151 H152 
+MOL_1:C16           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C15 C17 H161 H162 
+MOL_1:C17           C  c2      MOL  0  0   0.0200 0 0 8  1.0000  0.0000 C16 N2 H171 H172 
+MOL_1:N2            N  n       MOL  0  0  -0.5000 0 1 8  1.0000  0.0000 C17 C18 H2 
+MOL_1:C18           C  c'      MOL  0  0   0.3800 0 1 8  1.0000  0.0000 N2 O2/2.0 C19 
+MOL_1:O2            O  o'      MOL  0  0  -0.3800 0 0 8  1.0000  0.0000 C18/2.0 
+MOL_1:C19           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C18 C20 H191 H192 
+MOL_1:C20           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C19 C21 H201 H202 
+MOL_1:C21           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C20 C22 H211 H212 
+MOL_1:C22           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C21 C23 H221 H222 
+MOL_1:H221          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C22 
+MOL_1:H222          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C22 
+MOL_1:C23           C  c'      MOL  0  0   0.3800 0 1 8  1.0000  0.0000 C22 O3/2.0 N3/1.5 
+MOL_1:O3            O  o'      MOL  0  0  -0.3800 0 0 8  1.0000  0.0000 C23/2.0 
+MOL_1:H1            H  hn      MOL  0  0   0.2800 0 0 8  1.0000  0.0000 N1 
+MOL_1:H121          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C12 
+MOL_1:H122          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C12 
+MOL_1:H131          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C13 
+MOL_1:H132          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C13 
+MOL_1:H141          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C14 
+MOL_1:H142          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C14 
+MOL_1:H151          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C15 
+MOL_1:H152          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C15 
+MOL_1:H161          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C16 
+MOL_1:H162          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C16 
+MOL_1:H171          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C17 
+MOL_1:H172          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C17 
+MOL_1:H2            H  hn      MOL  0  0   0.2800 0 0 8  1.0000  0.0000 N2 
+MOL_1:H191          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C19 
+MOL_1:H192          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C19 
+MOL_1:H201          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C20 
+MOL_1:H202          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C20 
+MOL_1:H211          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C21 
+MOL_1:H212          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C21 
+MOL_1:N3            N  n       MOL  0  0  -0.5000 0 1 8  1.0000  0.0000 C23/1.5 C24 H3 
+MOL_1:C24           C  c2      MOL  0  0   0.0200 0 0 8  1.0000  0.0000 N3 C25 H241 H242 
+MOL_1:C25           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C24 C26 H251 H252 
+MOL_1:C26           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C25 C27 H261 H262 
+MOL_1:C27           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C26 C28 H271 H272 
+MOL_1:C28           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C27 C29 H281 H282 
+MOL_1:C29           C  c2      MOL  0  0   0.0200 0 0 8  1.0000  0.0000 C28 N4 H291 H292 
+MOL_1:N4            N  n       MOL  0  0  -0.5000 0 1 8  1.0000  0.0000 C29 C30 H4 
+MOL_1:C30           C  c'      MOL  0  0   0.3800 0 1 8  1.0000  0.0000 N4 O4/2.0 C31 
+MOL_1:O4            O  o'      MOL  0  0  -0.3800 0 0 8  1.0000  0.0000 C30/2.0 
+MOL_1:C31           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C30 C32 H311 H312 
+MOL_1:C32           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C31 C33 H321 H322 
+MOL_1:C33           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C32 C34 H331 H332 
+MOL_1:C34           C  c2      MOL  0  0  -0.2000 0 0 8  1.0000  0.0000 C33 C35 H341 H342 
+MOL_1:C35           C  c'      MOL  0  0   0.4500 0 1 8  1.0000  0.0000 C34 O5 O6/2.0 
+MOL_1:O5            O  o-      MOL  0  1- -0.5000 0 0 8  1.0000  0.0000 C35 
+MOL_1:H3            H  hn      MOL  0  0   0.2800 0 0 8  1.0000  0.0000 N3 
+MOL_1:H241          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C24 
+MOL_1:H242          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C24 
+MOL_1:H251          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C25 
+MOL_1:H252          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C25 
+MOL_1:H261          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C26 
+MOL_1:H262          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C26 
+MOL_1:H271          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C27 
+MOL_1:H272          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C27 
+MOL_1:H281          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C28 
+MOL_1:H282          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C28 
+MOL_1:H291          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C29 
+MOL_1:H292          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C29 
+MOL_1:H4            H  hn      MOL  0  0   0.2800 0 0 8  1.0000  0.0000 N4 
+MOL_1:H311          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C31 
+MOL_1:H312          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C31 
+MOL_1:H321          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C32 
+MOL_1:H322          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C32 
+MOL_1:H331          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C33 
+MOL_1:H332          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C33 
+MOL_1:H341          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C34 
+MOL_1:H342          H  h       MOL  0  0   0.1000 0 0 8  1.0000  0.0000 C34 
+MOL_1:O6            O  o-      MOL  0  0  -0.5000 0 0 8  1.0000  0.0000 C35/2.0 
+MOL_1:N5            N  n4      MOL  0  1+ -0.5000 0 0 8  1.0000  0.0000 C HN51 HN52 H53 
+MOL_1:HN51          H  hn      MOL  0  0   0.3600 0 0 8  1.0000  0.0000 N5 
+MOL_1:HN52          H  hn      MOL  0  0   0.3600 0 0 8  1.0000  0.0000 N5 
+MOL_1:H53           H  hn      MOL  0  0   0.3600 0 0 8  1.0000  0.0000 N5 
+
+
+#end
+

tools/msi2lmp/test/phen3_cff97.car

@@ -0,0 +1,29 @@
+!BIOSYM archive 3                                                               
+PBC=OFF                                                                         
+input file for discover                                                         
+!DATE Tue Jul 15 15:14:54 1997                                                  
+N        0.109592088   -0.199880913    0.000000478 PHEN 1      n+      N -0.0450
+HN1     -0.124733858   -1.202872038   -0.000001981 PHEN 1      h+      H  0.2800
+HN2     -0.285811990    0.244572327    0.840843439 PHEN 1      h+      H  0.2800
+HN3     -0.285812497    0.244576558   -0.840839982 PHEN 1      h+      H  0.2800
+CA       1.560634732   -0.038402185    0.000000465 PHEN 1      c       C -0.0780
+HA       1.972637177   -0.500293911    0.916701555 PHEN 1      h       H  0.0530
+C        1.942531705    1.422506809    0.000000450 PHEN 1      c-      C  0.2974
+OXT      3.187694550    1.672445178    0.000000438 PHEN 1      o-      O -0.5337
+O        1.070737839    2.346019268    0.000000449 PHEN 1      o-      O -0.5337
+CB       2.174581766   -0.718786478   -1.261021852 PHEN 1      c       C -0.1060
+HB1      1.839982390   -0.182426706   -2.172762394 PHEN 1      h       H  0.0530
+HB2      3.272250891   -0.569177628   -1.261509657 PHEN 1      h       H  0.0530
+CG       1.889680982   -2.218492746   -1.435816169 PHEN 1      cp      C  0.0000
+CD1      0.737977445   -2.629161119   -2.116767168 PHEN 1      cp      C -0.1305
+HD1      0.061427273   -1.894254208   -2.533302307 PHEN 1      h       H  0.1305
+CE1      0.424228579   -3.980331659   -2.214080095 PHEN 1      cp      C -0.1305
+HE1     -0.483345032   -4.285143852   -2.715474367 PHEN 1      h       H  0.1305
+CZ       1.268485427   -4.931880474   -1.646431088 PHEN 1      cp      C -0.1305
+HZ       1.020345688   -5.980008125   -1.718327641 PHEN 1      h       H  0.1305
+CE2      2.423752546   -4.531005859   -0.977356374 PHEN 1      cp      C -0.1305
+HE2      3.074717045   -5.268786907   -0.531340718 PHEN 1      h       H  0.1305
+CD2      2.733307123   -3.177516222   -0.869901538 PHEN 1      cp      C -0.1305
+HD2      3.619415522   -2.873045444   -0.331384182 PHEN 1      h       H  0.1305
+end
+end