SPICA: Surface Property fItting Coarse grAined model

Tutoriallipid membrane

Step 2. Convert PDB file to LAMMPS input file

In the previous step, we prepared the input PDB files either in CG (final.pdb) or AA (step5_assembly.pdb) format. Since LAMMPS reads its own formatted data file, it is required to convert the PDB file to LAMMPS data file. To convert CG PDB file, we provide a tool, called "setup_lammps". In the "CG PDB file LAMMPS input file" section, we will introduce how to use setup_lammps. To convert AA PDB file to LAMMPS data file, one can use CG-it, which was developed by Chris MacDermaid and Giacomo Fiorin. Check the details how to install and use it on the developer's Github page. We will breifly introduce how to use CG-it in this tutorial. The commands start with "$" and "%" in the gray source code box are for bash shell (or any linux shell) and TCL shell on VMD, respectively.

CG PDB file LAMMPS input file

To execute setup_lammps, one should provide the topology and number of molecules, database file, and input PDB file as arguments. For example, if the PDB file, named "final.pdb", contains 128 DOPC lipids and 3000 water molecules, the command will be:

$ setup_lammps DOPC.top 128 WAT.top 3000 spica_db.prm final.pdb

where the "DOPC.top" and "WAT.top" contain the topology of DOPC and water molecule, respectively. Topology files are included in the force field file (Check "./topology/*.top"). "spica_db.prm" is the force field file we provide. "final.pdb" is the PDB file contains the intial CG coordinates. 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

AA PDB file LAMMPS input file

To convert the AA PDB file to LAMMPS input file, we use CG-it. CG-it requires the parameter and topology files in json format. We also included these files in the force field file.
  1. Open "step5_assembly.pdb" file on VMD with its topology file "step5_assembly.psf". In case, only PDB file is availabe, one can easily generate PSF file using VMD plugin, called "Automatic PSF Builder". Please make sure that the PSF format is in CHARMM format. Because the topology file we provide follows the CHARMM format, if either atom name and type is wrong, then, the conversion will be failed.
    $ vmd step5_assembly.psf step5_assembly.pdb

  2. Open Tk console (Menu-Extensions-TkConsole). Load CG-it package and parameter files.
    % package require cgtools
    % cg readparam spica_par.json
    % cg readtop ./topology/spica_top.json

  3. Select atoms and convert to CG description.
    % sel atomselct ["all"]
    % cg map -sel $sel

  4. Recalculate the bonded interactions.
    % cg setbonds
    % cg setangles
    % cg setdihedrals
    % cg reanalyzemol

  5. Save converted files.
    % animate write psf system.cg.psf
    % animate write pdb system.cg.pdb
    % cg writelammpsdata system.cg.data full
    % cg writelammpsparam system.cg.param both

The output files "system.cg.data" and "system.cg.param" will be read in the LAMMPS input script.

We provide simple tcl script, which automatically executes above commands. Once you load AA coordinate and topology, run the cg_it.tcl script by invoking "source cg_it.tcl". Please make sure that the location of JSON files are correct in the TCL file.

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SPICA Force Field

Nagoya University