forked from lijiext/lammps
some more updates to the README file to reflect the inclusion of the CMAP example and renamed file names
This commit is contained in:
Axel Kohlmeyer
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326fdf2cf1
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d7d321a512
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@ -8,7 +8,7 @@ lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
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In this directory, you should find:
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1) A perl script called "charmm2lammps.pl"
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2) A perl script called "lammps2pdb.pl"
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3) An "example" folder containing an example of how to use these tools.
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3) Two folders containing examples of how to use these tools.
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4) An "other" folder containing other potentially useful tools.
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In addition, you will need to provide the following input for
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@ -51,15 +51,16 @@ biomolecule and convert it into LAMMPS input, and then create a *.pdb
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trajectory from the LAMMPS output.
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1) Get the pdb file you want to model. http://www.rcsb.org/pdb/ For
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this example, we will use 1ac7.pdb
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this examples, we will use either 1ac7.pdb or 1gb1.pdb
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2) If there are multiple models in the pdb file, choose the one you
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want and delete the others. Save the pared-down file as 1ac7_pared.pdb
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3) Download the charmm FF files and choose the one you want from the
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tarball. We will use all27_na for this example.
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http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
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toppar_c31b1.tar.gz
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tarball. We will use all27_na for 1AC7 and all36_prot for 1GB1. The
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required files for the example are included in their folders. You can
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download complete CHARMM force field packages from:
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http://mackerell.umaryland.edu/charmm_ff.shtml
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4) Create a *.pgn file for use with psfgen (you will need to have VMD
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installed, http://www.ks.uiuc.edu/Research/vmd/ ). This is the hardest
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@ -84,20 +85,25 @@ writepdb 1ac7.pdb
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writepsf charmm 1ac7.psf
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exit
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5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
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For 1GB1 the corresponding 1gb1.psf file has been created with CHARMM-GUI,
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http://www.charmm-gui.org
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5) Type "vmd -dispdev none -e 1ac7.pgn" to build the 1ac7.psf file, and the new
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1ac7.pdb file.
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6) Run charmm2lammps.pl by typing:
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"perl charmm2lammps.pl all27_na 1ac7 -border=1 -pdb_ctrl -water -ions"
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"perl charmm2lammps.pl all27_na 1ac7 -border=2.0 -pdb_ctrl -water -ions"
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or
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"perl charmm2lammps.pl all36_prot 1gb1 -border=2.0 -cmap=36 -water -ions"
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7) Run lammps by typing: "lmp_mpi -in 1ac7.in"
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7) Run lammps by typing: "lmp_mpi -in 1ac7.in" or "lmp_mpi -in 1gb1.in"
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8) Run lammps2pdb.pl by typing: "perl lammps2pdb.pl 1ac7"
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** Additional notes:
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The charmm2lammps.pl script takes the pdb and psf files for the 1ac7
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molecule and converts them into LAMMPS format. The -water option
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or 1gb1 molecules and converts them into LAMMPS format. The -water option
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embeds the molecule in water on a crystal lattice. The -border option
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includes a layer of water surrounding the minimum dimensions of the
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molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
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@ -107,22 +113,22 @@ after the # sign is a comment) for user convenience in tracking atom
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types etc. according to CHARMM nomenclature. If this is not desired,
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the -nohints option can be used to turn off this function.
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The example molecule provided above (i.e., 1ac7) is a DNA fragment.
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If instead, a peptide longer than 2 amino acid residues or a protein
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is to be modeled, the '-cmap' option should be used. This will add a
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section at the end of the data file with the heading of 'CMAP' that
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The provided 1ac7 example molecule is a DNA fragment. For peptides
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longer than 2 amino acid residues or a protein is to be modeled,
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e.g. the 1gb1 binding domain of a protein, the '-cmap' option should
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be used. This will add CMAP section at the end of the data file that
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will contain cmap crossterm corrections for the phi-psi dihedrals for
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the amino acid residues. You will then need to also copy the
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appropriate file for the cmap crossterms into your directory and be
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sure that you are using the appropriate cmap crossterms that go with
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the respective version of the charmm force field that is being used
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(e.g, cmap22.data or cmap36.data). This is necessary to account for
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the fact that the CHARMM group has provided updated cmap correction
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(e.g, charmm22.cmap or charmm36.cmap). This is necessary to account
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for the fact that the CHARMM group has provided updated cmap correction
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terms for use with the c36 and more recent version of the charmm
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protein force field. Copies of cmap22.data and cmap36.data are
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provided in the tools/ch2lmp directory.
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protein force field. Copies of charmm22.cmap and charmm36.cmap are
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provided in the potentials directory.
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The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
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The default timestep in the LAMMPS *.in file is set to 1.0 fs, which
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can typically be increased to 2 fs after equilibration if the bonds
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involving H are constrained via shake. Also, after equilibration, the
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delay on neigh_modify can probably increased to 5 or so to improve
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