Step 3. Convert PDB file to LAMMPS input file
In the previous step, we prepared the topology file (protein.cg.top) needed for generating LAMMPS input files for CG-MD simulations.
As seen in tutorial for lipid membrane systems
, to convert CG PDB file to LAMMPS data file and gain LAMMPS parameter file from database file of SPICA FF for protein, we use a tool "setup_lammps".
download Database file for SPICA protein
In this tutorial, the command line to excute the "setup_lammps" is:
$ setup_lammps protein.cg.top 1 DOPC.top 128 WAT.top 2134 CLA.top 4 spica_protein_db.prm system.cg.pdb
where the "DOPC.top", "WAT.top", and "CLA.top" contain the topology of DOPC, water, and chloride ion, respectively. These topology files are included in the force field file (Check "./topology/*.top"). "spica_protein_db.prm" is the force field file we provide. "system.cg.pdb" is the PDB file contains the intial CG coordinates generated in Step 1 of this tutorial
. One should be careful with the order of arguments. Especially, molecule topology and number should be the same as in the PDB file.
If the conversion is successful, setup_lammps will generate two output files, "DATA.FILE", and "PARM.FILE". The input script will read these files. The contents of "DATA.FILE" can be visualized on VMD with Topotools
% package require topotools
% topo readlammpsdata DATA.FILE
In addition, the "setup_lammps" (v2.0) gives PSF file of the target system. We can visualize the system using the output PSF file (out.psf) and input PDB file (system.cg.pdb):
$ vmd out.psf system.cg.pdb