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spica-tools

DOI
This repository provides tools to set up coarse-grained (CG) molecular dynamics (MD) simulation using the SPICA force field and tools to support SPICA CG parametrization. The tools are written in Python and can be invoked with the below commands. Members of the SPICA group developed the tool; for more information about the SPICA force field and its development members, visit the SPICA website.

Installation

The command to invoke the tools in the src/ directory is cg_spica and requires the Python 3 environment. You will need a bash environment to execute the tools using the commands in a console. You can download this repository, including the setup file to use the command, with the following command:

git clone git@github.com:SPICA-group/spica-tools.git

Then, change the current directory to the top directory of the repository:

cd spica-tools/

There is a bash script set.sh to add the path to use the command, and run it with the following command:

source set.sh

The path to cg_spica has been added to the PATH environmental variable. Adding the above line to a configuration file such as .bash_profile may be useful if you need to use the spica-tools frequently. To verify that the commands to integrate python codes in the src/ directory is available in the console, run the following commands:

cg_spica -h  
cg_spica map2cg -h

You can see the available options for the commands, if the command path is properly added to the PATH.
Cg_spica requires several python libraries to execute some codes, including arithmetic operations, and to read trajectory files obtained from MD simulations. These libraries are listed in requirements.txt in the top directory and can be installed using pip with the following command:

pip install -r requirements.txt

Documentation

The above spica-tools documentation can be found here. You can create the documentation on your machine with the following commands:

cd doc/  
make html

Tools

  • Python (in src/, can be used with cg_spica)
    • json2top : create the top files needed for the setup_*** programs from a json file with SPICA mapping information
    • map2cg : map AA configuration to CG, available only in PDB format
    • maptraj : map AA MD trajectories to CG, requires MDAnalysis module
    • modion : adjust NaCl salt concentration in CG configuration
    • ENM : generate top files of protein with elastic networks
    • Go : generate top files of protein with Go model
    • wat2polar : convert SPICA CG water to pSPICA polar CG water
    • setup_lmp : generate input files to run CG-MD with LAMMPS
    • setup_gmx : generate input files to run CG-MD with GROMACS
      Apply the patch file distributed in the repository of SPICA-group (gromacs-spica) to GROMACS software to make it useful for the MD with SPICA-FF
    • gen_lmpin : generate a LAMMPS input file for SPICA or pSPICA
    • gen_gmxin : generate GROMACS input files for SPICA or pSPICA

License

Tools included in this repository are distributed under the MIT license.

Copyright (c) 2022 SPICA-group

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.