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GMXAnalysis

For the purpose of post progressing of MD carried by gromacs
This repository is used to store some useful scripts for MD analysis.

Content:

  • DCCM.py: a python script to read xtc and generate the DCCM(Dynamical Cross-Correlation Matrix) automatically
  • tpr2gro.py: generate the gro file from tpr file (tpr should be converted )
  • genxyz_gui.py: generate a set of gaussian input files for rigid scan
  • ss.py/ss.jl: generate a secondary structure map with the file generated by dssp
  • MMPBSAv1.7: [under development] to calculate protein/ligand binding energy. only need tpr xtc ndx file. current support calculate MM\PB\SA\entropy contribution\Debek Huckell Correction. To do: (1) specify differnt radius(current:mbondi) (2) normal mode analysis (3) calculate with diffenert Dielectric constant。
  • mdana: [not yet started] a md analysis script written in rust.

Usage:

DCCM.py

required packages:

  • pandas
  • matplotlib
  • numpy
  • sys
  • mdanalysis

command:
python DCCM.py md.gro md.xtc

tpr2gro.py

you should use gmx dump command to convert .tpr file to readable out file.
Then use the command below:
command:
python tpr2gro.py md.out

genxyz_gui.py

This script is used to generate a set of gaussian input files from the molecule initial position to the end position for the purpose of rigid scanning. no-gui version is also provided.

required packages:

  • numpy
  • pandas
  • math

command:
python genxyz_gui.xyz

ss.py/ss.jl

This script is used to generate a picture of protein's secondary structure. Meanwhile, it needs the program dssp to generate the assignment file xx.dssp It only works for proteins which contains less than 500 amino acids.

required packages: python ver.

  • matplotlib 3.5.2
  • dssp 3.0.0 julia ver.
  • luxor

command:
python ss.py xx.dssp julia ss.jl xx.dssp