gmxpla

Gromax protein-ligand MD trajectory analysis tools to obtain csv and png file summary of protein-ligand interaction energy, ligand RMSD, and ligand RMSF.

Licence

This package is distributed under the MIT License.

Tutorial

You can try tutorial of meekovina to know how to install and run:
https://colab.research.google.com/github/mkatouda/gmxpla/blob/main/gmxpla_tutorial_jp.ipynb

Required softwares

1. python: 3.7 or later
2. pyyaml (https://pyyaml.org/)
3. matplotlib (https://matplotlib.org/)
4. gromacs (https://www.gromacs.org/)

Installation

Install gromacs

See install guide: https://manual.gromacs.org/current/install-guide/index.html

Install from github

pip install git+https://github.com/mkatouda/gmxpla.git

Local install

git clone https://github.com/mkatouda/gmxpla.git
cd gmxpla
pip install .

Command usage

usage: gmxpla [-h] [-i INP] [-e EDR] [-t TPR] [-x XTC] [-n NDX] [-oc OUTCSV] [-v]

optional arguments:
  -h, --help            show this help message and exit
  -i INP, --inp INP     yaml style input file, overwriting argument values (default: None)
  -e EDR, --edr EDR     Gromacs energy file (edr file) (default: None)
  -t TPR, --tpr TPR     Gromacs topology file (tpr or gro file) (default: None)
  -x XTC, --xtc XTC     Gromacs trajectory file (xtc file) (default: None)
  -n NDX, --ndx NDX     Gromacs index file (ndx file) (default: None)
  -oc OUTCSV, --outcsv OUTCSV
                        docking score output (csv file) (default: docking_score.csv)
  -v, --verbose         Verbose output. (default: False)

Exmaples of command line usage

gmxpla -e prod.edr -t prod.tpr -x prod.xtc -n index.ndx -oc prod_docking_score.csv

Exmaples of yaml input usage

Prepare input yaml file input.yml:

edr: './prod.edr'
tpr: './prod.tpr'
xtc: './prod.xtc'
ndx: './index.ndx'
outcsv: './prod_docking_score.csv'
verbose: False

Then, run gmxpla in command line:

gmxpla -i input.yml

Keywards of yaml file are the same in the name of command line options.
See above explation of command line options.

Author

Michio Katouda (katouda@rist.or.jp)