see the MM/GB(PB)SA介绍
apt-get update
apt install gromacsconda create -n amber21 -c conda-forge ambertools=21 gmx_MMPBSA=1.5.2 acpype=2021.02
python setup.py install- If you have the gromacs topology and index files. Just use the
hmtpbsa-traj
hmtpbsa-traj -h
usage: hmtpbsa-traj [-h] -i INP -p TOP -ndx NDX [-m {gb,pb,pb+gb,gb+pb}] [-t TRAJ] [-indi INDI] [-dec] [-D]
Free energy calcaulated by PBSA method.
optional arguments:
-h, --help show this help message and exit
-i INP A pdb file or a tpr file for the trajectory.
-p TOP Gromacs topol file for the system.
-ndx NDX Gromacs index file, must contain recepror and ligand group.
-m {gb,pb,pb+gb,gb+pb}
Method to calculate: gb, pb, pb+gb. default:gb
-t TRAJ A trajectory file contains many structure frames. File format: xtc, pdb, gro...
-indi INDI External dielectric constant. detault: 1.0
-dec Decompose the energy. default:false
-D DEBUG model, keep all the files.
- If you want do minimization or MD simulation for the complex. Just use the
hmtpbsa-pipeline
hmtpbsa-pipeline -h
usage: hmtpbsa-pipeline [-h] -i RECEPTOR [-l LIGAND [LIGAND ...]] [-c CONFIG] [-d LIGDIR] [-f PBSAFILE] [-o OUTFILE]
GBSA Calculation.
optional arguments:
-h, --help show this help message and exit
-i RECEPTOR Input protein file with pdb format.
-l LIGAND [LIGAND ...]
Ligand files to calculate binding energy.
-c CONFIG Configue file, default: /opt/anaconda3/envs/amber/lib/python3.8/site-packages/hmtpbsa-0.0.2-py3.8.egg/hmtpbsa/data/default.ini
-d LIGDIR Floder contains many ligand files. file format: .mol or .sdf
-f PBSAFILE gmx_MMPBSA input file. default=None
-o OUTFILE Output file.- Give a protein and some ligand files. Obtain the binding energy with
hmtpbsa-pipeline
hmtpbsa-pipeline -i ./example/2fvy/protein.pdb -l ./example/2fvy/BGC.mol2- Calculate PBSA value with
hmtpbsa-traj
hmtpbsa-traj -i example/3f/complex.pdb -p example/3f/complex.top -ndx example/3f/index.ndx -m pb gb -t example/3f/complex.pdb