Brief description of tools/files:
gmx_MMPBSA (Getting started - gmx_MMPBSA Documentation) is a new tool based on AMBER’s MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. It works with all GROMACS versions along with AmberTools20 or 21 and brings improvements in compatibility, versatility, analyses, and parallelization compared to existing programs.
Several calculations can be performed with gmx_MMPBSA, including but not limited to:
- Normal binding free energies
- Stability
- Alanine scanning
- Entropy corrections
- Decomposition schemes
- QM/MMGBSA
Link: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/getting-started
Contact person (name and email address): Mario S. Valdes Tresanco (mariosergiovaldes145@gmail.com)
How the work has been tested/reviewed: A number of examples are provided at: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples
don’t hesitate to contact us if you have any questions :)
cheers!
2 Likes
Can this tool use for the protein and peptide complex binding free energy calculation and performing alanaine scanning as well. i am facing issue while treating peptide as ligand :
gmx_MMPBSA -O -i mmpbsa.in -cs md_50ns.tpr -ci index.ndx -cg 18 17 -ct final.xtc
[INFO ] Starting gmx_MMPBSA 1.6.4+15.ge8187141 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_50ns.tpr -ci index.ndx -cg 18 17 -ct final.xtc [INFO ] Checking mmpbsa.in input file… [INFO ] Checking mmpbsa.in input file…Done. [INFO ] Checking external programs… [INFO ] cpptraj found! Using /home/megha/miniconda3/envs/py3.11/bin/cpptraj [INFO ] tleap found! Using /home/megha/miniconda3/envs/py3.11/bin/tleap [INFO ] parmchk2 found! Using /home/megha/miniconda3/envs/py3.11/bin/parmchk2 [INFO ] sander found! Using /home/megha/miniconda3/envs/py3.11/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /usr/local/gromacs/bin/gmx [INFO ] Checking external programs…Done. [INFO ] Building AMBER topologies from GROMACS files… [INFO ] Get PDB files from GROMACS structures files… [INFO ] Making gmx_MMPBSA index for complex… [INFO ] Normal Complex: Saving group chB_chA (18_17) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] No receptor structure file was defined. Using ST approach… [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Receptor: Saving group chB (18) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [INFO ] No ligand structure file was defined. Using ST approach… [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal Ligand: Saving group chA (17) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency… [INFO ] [INFO ] Generating AMBER Compatible PDB Files… [INFO ] Changing the Complex residues name format from GROMACS to AMBER… [INFO ] Changing the Receptor residues name format from GROMACS to AMBER… [INFO ] Changing the Ligand residues name format from GROMACS to AMBER… [INFO ] Splitting receptor and ligand in PDB files.. [INFO ] Building tleap input files… [ERROR ] MMPBSA_Error /home/megha/miniconda3/envs/py3.11/bin/tleap failed when querying _GMXMMPBSA_leap.in Check the gmx_MMPBSA.log file to report the problem. File "/home/megha/miniconda3/envs/py3.11/bin/gmx_MMPBSA", line 33, in <module> sys.exit(load_entry_point('gmx_MMPBSA==1.6.4+15.ge8187141', 'console_scripts', 'gmx_MMPBSA')()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 128, in buildTopology tops = self.makeToptleap() ^^^^^^^^^^^^^^^^^^^ File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 1611, in makeToptleap self._run_tleap(tleap, 'leap.in', data_path) File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 1744, in _run_tleap GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + arg1)) File "/home/megha/miniconda3/envs/py3.11/lib/python3.11/site-packages/GMXMMPBSA/exceptions.py", line 171, in _init_ raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/megha/miniconda3/envs/py3.11/bin/tleap failed when querying _GMXMMPBSA_leap.in
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.