gmx-polymer-tools

Perl scripts for polymer modeling using GROMACS

Functions

These Perl scripts help to model synthetic polymers using GROMACS

These are

• mol22rtp.pl : translates sybyl-mol2 format file (*.mol2) to GROMACS residue topology format file (*.rtp)

• rtp2tmer.pl : translates plain rtp format file (*.rtp) of trimer to real rtp file (*.rtp)

• rtp2hdb.pl : create hydrogen databese file (*.hdb) for the terminal residues from the real rtp file (*.rtp)

• pdb2tmer.pl : create plain pdb format file (*.pdb) of trimer to the trimer pdb file (*.pdb) for pdb2gmx

• cn-term.pl : translate pdb file's the first and the last residues to be the terminal residues.

And additionally,

• ambdat2gmx.pl : translates AMBER force field parameter file (*.dat) to GROMACS forcefiled data files (*.itp, *.atp)

• frcmod2gmx.pl :translates AMBER parameter modification file (*.frcmod) to GROMACS forcefiled data files (*.itp, *.atp).

These two scripts are not specifically for polymer modeling, but help to provide general AMBER (GAFF) force fields for GROMACS pdb2gmx.

Usage

mol22rtp.pl < 3lla.mol2 > 3lla.rtp

Input *.mol2 file is assumed to be generated with antechamber with proper force field (e.g. GAFF) atom types and charges.

Resultant plain *.rtp file can be input for rtp2tmer.pl as,

rtp2tmer.pl -n 7 -c 29 < 3lla.rtp > lla.rtp

Resultant lla.rtp is the final residue topology files for the monomar (here lla, L-lactic acid) as new residue.

Corresponding hydrogen databese file (*.hdb) for the terminal residues can be created from this rtp file.

rtp2hdb.pl < lla.rtp > lla.hdb

Trimer pdb file (3lla.pdb) can be translated to the pdb file suitable for pdb2gmx by

pdb2tmer.pl -n 7 -c 29 < 3lla.pdb > 3lla_4pdb2gmx.pdb

Simple 60 mer pdb file (60lla.pdb) can be translated with

cn-term.pl < 60lla.pdb > 60lla_4pdb2gmx.pdb

to obtain pdb file suitable for pdb2gmx as

gmx pdb2gmx -f 60lla_4pdb2gmx.pdb -o 60lla.gro -ff gaff -water none

An example of these modeing flow can be found in this tutorial (in Japanese).

To obtain GROMACS force field data files (in gaff.ff directory) from AMBER force field prarameter file for general AMBER force field (GAFF),

mkdir gaff.ff && cd gaff.ff

ambdat2gmx.pl < gaff.dat

This creates

• atomtypes.atp

• ffbonded.itp

• ffnonbonded.itp

• forcefield.doc

• forcefield.itp

Resultant gaff.ff can be used for pdb2gmx.

To obtain GROMACS force field data files from AMBER parameter modification file,

frcmod2gmx.pl < 3lla.frcmod

This creates

• frcmod_atomtypes.atp

• frcmod_ffbonded.itp

• frcmod_ffnonbonded.itp

Prerequisites

Perl interpleater.

Authors

Makoto Yoneya.