error mmgbsa

[negin safaee]

Hi gmx-mmpbsa users, I wanted to calculate free energy binding for my protein complex but i got following error:

gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.pdb -ci index2.ndx -cg 16 19 -ct traj20-50.xtc -cp topol.top
[INFO   ] Starting
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.pdb -ci index2.ndx -cg 16 19 -ct traj20-50.xtc -cp topol.top

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/cpptraj
[INFO   ] tleap found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/tleap
[INFO   ] parmchk2 found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/parmchk2
[INFO   ] sander found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...
[INFO   ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 16_19 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 Complex: Saving group 16 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 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Building Normal Complex Amber Topology...
  File "/home/safaei/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
    app.make_prmtops()
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 598, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 311, in read
    molecule.add_atom(*self._parse_atoms(line, params))
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 492, in _parse_atoms
    return atom, words[3], int(words[2])
ValueError: invalid literal for int() with base 10: '82A'
Exiting. All files have been retained.

I would be so thankful if you could help me to solve the problem.

[Mario Sergio Valdes]

This error is because you are using an outdated version of ParmEd, update it like this

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

or

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

depending on the installation methods you have used.

gmx_MMPBSA v1.4.3 will be discontinued shortly. We recommend you to use version v1.5.5 which is better optimized and has more tools and methods.

Mario S.

[negin safaee]

Thank you for your response. When I used these commands that you mentioned i got the following error:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
  Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-qb507h8a
  ERROR: Error [Errno 2] No such file or directory: 'git' while executing command git version
ERROR: Cannot find command 'git' - do you have 'git' installed and in your PATH?

and:

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

amber.python: command not found

[Mario Sergio Valdes]

Please, install git

    sudo apt install git 

or  

   conda install -c anaconda git

Then install PamEd

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4 - U

[negin safaee]

I am so thankful that you helped me to solve the problem. I used the commands that you mentioned and It worked well.

Best wishes

safaee