SPICA: Surface Property fItting Coarse grAined model

Tutorialprotein

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

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SPICA Force Field

Research Institute for Interdisciplinary Science (RIIS)
Okayama University