Requirements

• GROMACS
• Python
• Snakemake
• Sobtop (For generating small molecule topology files)
• s_mmpbsa (For calculating mmpbsa)

Acknowledgements

Sobtop: This workflow uses Sobtop_1.0(dev5) developed by Dr. Tian Lu for generating small molecule topology files. If you use this workflow in your research, please cite Sobtop as:

Tian Lu, Sobtop, Version [sobtop_1.0(dev5)], http://sobereva.com/soft/Sobtop (accessed on 24-12-2024)

s_mmpbsa: This workflow uses s_mmpbsa-0.6.7 developed by [email protected] for calculating mmpbsa.

Usage

1. Configure input files: Edit config.yaml to set input file paths:

   protein_file: "input/protein.pdb"
   ligand_file: "input/ligand.pdb"
   cofactor_file: "input/cofactor.pdb"

2. Run simulation:

   snakemake 

Scripts Description

add_itp.py

• Purpose: Add ITP files to topology file
• Usage: python add_itp.py -l <itp_files> -p <topology_file>

add_posre.py

• Purpose: Add position restraints to topology file
• Usage: python add_posre.py -l <posre_files> -p <topology_file>

merge_gro.py

• Purpose: Merge multiple GRO files
• Usage: python merge_gro.py -p <protein_gro> -l <ligand_gros> -o <output_gro>

merge_itp.py

• Purpose: Merge ligand ITPs with protein topology
• Usage: python merge_itp.py -lp <ligand_itps> -p <protein_top>

extract.py

• Purpose: Extract topology sections
• Usage: python extract.py -i <input_file> -o <output_file>

run_mmpbsa.py

• Purpose: Automate MM-PBSA calculations using s_mmpbsa
• Usage: python run_mmpbsa.py -t <tpr_file> -x <xtc_file> -n <ndx_file> -p <protein_group> -l <ligand_group> -i <interval>
• Parameters:
  • -t, --tpr: Input tpr file from MD simulation
  • -x, --xtc: Input trajectory file
  • -n, --ndx: Input index file
  • -p, --protein: Protein group number in index file
  • -l, --ligand: Ligand group number in index file
  • -i, --interval: Analysis interval in ns (default: 1)