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SPICA: Surface Property fItting Coarse grAined model

Downloads

Parameter and topology files

SPICA

  • spica_v1.1.tar.gz -- DOWNLOAD
  • spica_v1.tar.gz -- DOWNLOAD
  • Version history
    [28.08.18] v1.0 -- First release.
    [01.05.22] v1.1 -- Second release. This includes protein model.
  • v1.1 Files:
    - spica_db.prm: Official SPICA force field file. This file can be read by setup_lammps
    - spica_par.json: JSON formatted force field file for CG-it
    - ./topology/*.top: Topology files for setup_lammps
    - ./topology/spica_top.json: Topology files for CG-it
  • v1.0 Files:
    - spica_db.prm: Official SPICA force field file. This file can be read by setup_lammps
    - spica_par.json: JSON formatted force field file for CG-it
    - ./topology/*.top: Topology files for setup_lammps
    - ./topology/spica_top.json: Topology files for CG-it

Files for LAMMPS

Setup lammps

  • setup_lammps v2.0 -- DOWNLOAD
  • Version history
    [28.08.18] v1.0 -- First release (originally coded by Russell DeVane and modified by others)
    [13.01.20] v2.0 -- Second release. PSF file is outputted in addtion to LAMMPS input files.
  • How to use:
    - Untar the attached file and invoke "make" on linux shell. You will see the executable binary file, "setup_lammps".

    -
    Usage:
     setup_lammps <MOL_1.top> <N_MOL_1> [ <MOL_2.top> <N_MOL_2> . . . <MOL_n.top> < N_MOL_n> ] <param file> <coord file>
    • MOL_1.top, MOL_2.top, ... , MOL_n.top: Molecule topology file name (included in the force field file.)
    • N_MOL_1, N_MOL_2, N_MOL_n: Number of each molecule
    • param file: Force field parameter file: spica_db.prm (included in the force field file.)
    • coord file: Coordindate file name (in PDB format) 
    -
    Output files:
    • DATA.FILE: LAMMPS formatted coordinate file
    • PARM.FILE: LAMMPS formatted parameter file
    • out.psf: PSF formatted topology file
  • Please refer to the tutorial for further details.

Other tools for SPICA FF

CG Mapping

  • map_to_cg.py v1.0 -- DOWNLOAD
  • Version history
    [13.01.20] v1.0 -- First release (originally coded by Russell DeVane and modified by others)
  • How to use:
    - This can work with PYTHON2.6 or higher version, and reads "spica_top.json" (included in the force field file). When this script is excuted, you must put the json file on a current dirrectory.

    -
    Usage:
     map_to_cg.py <AA coord file> <CG coord file>
    • AA coord file: Input AA coordindate file name (in PDB format) 
    • CG coord file: Output CG coordindate file name (in PDB format) 

    Generate protein topology and Apply elastic network to protein

  • gen_top_elastic_network.py v1.0 -- DOWNLOAD
  • Version history
    [13.01.20] v1.0 -- First release (originally coded by Russell DeVane and modified by others)
  • How to use:
    - This can work with PYTHON2, and provides only CG protein topology files.

    -
    Usage:
     gen_top_elastic_network.py <CG coord file > <CG topology file>
    • CG config file: Input CG coordindate file name (in PDB format) 
    • CG config file: Output CG topology file name (in the same format as topology files for "setup_lammps") 
  • Please refer to the tutorial for further details.

pSPICA

pSPICA parameters

  • pSPICA_protein.prm v1.1 -- DOWNLOAD for lipid and protein
  • pSPICA_lipid.prm v1.0 -- DOWNLOAD for lipid

WAT2PWAT.py

  • WAT2PWAT.py v1.0 -- DOWNLOAD
  • How to use:
    -
    Usage:
     WAT2PWAT.py input_Configuration_file output_Configuration_file
    • input/output_Configuration_file = Path to input/output configuration_file. File in PDB format
    -
    Output files:
    • output_Configuration_file: PDB file where uncharged CG water is replaced with polar CG water

convert_PARM.py

  • convert_PARM.py v1.0 -- DOWNLOAD
  • How to use:
    -
    Usage:
     convert_PARM.py input_Parameter_file output_Parameter_file
    • input/output_Parameter_file = Path to input/output parameter_file. File in LAMMPS format
    -
    Output files:
    • output_Parameter_file: LAMMPS formatted parameter file to use tabulated potentials for polar CG water
  • Please refer to the tutorial for further details here.

tSPICA

tSPICA Coefficents

  • tSPICA_Coeffs.txt v1.0 -- DOWNLOAD
  • Description of formatting here

tSPICA.py

  • tSPICA.py v1.0 -- DOWNLOAD
  • How to use:
    -
    Usage:
     tSPICA.py <temperature> <pressure> <parameter_file> <coefficients_file>
    • temperature: Given in K
    • pressure: Given in MPa
    • parameter_file: Parameter file for LAMMPS
    • coefficients_file: tSPICA coefficient file
    -
    Output files:
    • t-parameter_file: updated parameter file for tSPICA
  • Please refer to the tutorial for further details here.

SPICA Force Field

Okayama University