diff --git a/tools/amber2lmp/amber2lammps.py b/tools/amber2lmp/amber2lammps.py
index cc74cf2bb2..16b8ded46a 100644
--- a/tools/amber2lmp/amber2lammps.py
+++ b/tools/amber2lmp/amber2lammps.py
@@ -1,1009 +1,1008 @@
-#! /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
-# Bug Fixed :Third argument in Dihedral Coeffs section is an integer - Ketan S Khare September 26, 2011
-# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer vesions of .top and .crd files in amber12. 
-
-#============================================================
-
-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] = int(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 Number...'
-        self.ANUMBER = []
-      	for i in range(self.NATOM):
-            self.ANUMBER.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 1-4 Electrostatic Scaling Factor...'
-        self.SCEEFAC = []
-        for i in range(self.NPTRA):
-            self.SCEEFAC.append(eval(Pop(Item_list,0)))
-        
-	print 'Reading 1-4 Van der Waals Scaling Factor...'
-        self.SCNBFAC = []
-        for i in range(self.NPTRA):
-            self.SCNBFAC.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()
+#! /usr/bin/evn python2
+
+# 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
+# Bug Fixed :Third argument in Dihedral Coeffs section is an integer - Ketan S Khare September 26, 2011
+# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer vesions of .top and .crd files in amber12. 
+
+#============================================================
+
+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] = int(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 Number...'
+        self.ANUMBER = []
+      	for i in range(self.NATOM):
+            self.ANUMBER.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 1-4 Electrostatic Scaling Factor...'
+        self.SCEEFAC = []
+        for i in range(self.NPTRA):
+            self.SCEEFAC.append(eval(Pop(Item_list,0)))
+        
+	print 'Reading 1-4 Van der Waals Scaling Factor...'
+        self.SCNBFAC = []
+        for i in range(self.NPTRA):
+            self.SCNBFAC.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()