Error in MMGBSA protein-protein complex

[negin safaee]

Hello everyone,

I am trying to do MM(GB) SA calculation by gmx_MMPBSA but I have got the following error, I also cut my xtc file . I think It could be related to '82A' in my topology file but I don't know how to solve it. Please help me to solve this problem.

  gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index2.ndx -cg 16 17 -ct pu.xtc -cp topol.top
[INFO   ] Starting
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index2.ndx -cg 16 17 -ct pu.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/local/gromacs/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_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 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 17 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 have also attached the files.

[Mario Sergio Valdes]

This error itself is not from gmx_MMPBSA but from ParmEd. Since last year I reported the bug (https://github.com/ParmEd/ParmEd/issues/1153). This error only occurs when the topology contains insertion codes and the topology conversion mode is used (if the -cp option was defined) of gmx_MMPBSA. If you use AMBER ff, it is possible to get around the problem by not defining the -cp option, however, for CHARMM ff, we have no solution. We will try to contact the ParmEd developers in order to collaborate on the solution to this error.

Sincerely

Mario S.

[Mario Sergio Valdes]

In order not to leave you with uncertainty, I decided to do some things. I created a Pull Request on Github solving the problem (hopefully for the new version they will have accepted it). I also created a fork of ParmEd and made the modifications. To update ParmEd do the following:
- conda create -n gmxMMPBSA_fixed_ParmEd (Create a new conda environment, to avoid compatibility problems)
- conda activate gmxMMPBSA_fixed_ParmEd
- conda install -c conda-forge mpi4py ambertools=21 compilers
- pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd -U (updates ParmEd from my Github fork)
- python -m pip install PyQt5 gmx_MMPBSA

In principle, it should work without problems, but keep in mind that this is experimental.
Tell me if you could do the calculations

Mario S.

[Mario Sergio Valdes]

We have been working on this solution. The instructions remain the same, with only minor modifications.

1. conda create -n gmxMMPBSA python=3.9 (Create a new conda environment, to avoid compatibility problems)
2. conda activate gmxMMPBSA

1. conda install -c conda-forge mpi4py ambertools=21 compilers

1. pip install git+https://github.com/ParmEd/ParmEd@v3.4 -U (updates ParmEd from the official Github repository, since they accept the PR)

1. python -m pip install PyQt5 gmx_MMPBSA

Now work as expected!

Sincerely.

Mario S.

[negin safaee]

Thank you very much for your response

If I run these commands in the terminal, May my system and the Python I have installed crash? or may Cause a problem in my installed Program? Because I am a beginner in this field and I use the VMware virtual machine installed on my computer.

Thanks a lot

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[Mario Sergio Valdes]

Not at all. In fact, the advantage that conda offers is the creation of environments that allow a set of packages to be isolated, reducing incompatibilities between the dependencies of other programs. This also allows you to enjoy different versions of the same program simply by creating an environment for each version. Keep in mind that conda manages its own python interpreter, so both your OS and system python should not have any problems or incompatibility. I invite you to learn about conda, since I found it and learned how to handle it, life is easier.

If you have conda installed, follow the steps that I mention, which will make you have the gmxMMPBSA environment independent of the rest of the installations. To use the gmx_MMPBSA just activate the environment (conda activate gmxMMPBSA) in a terminal. To use the base conda environment, deactivate the current environment (conda deactivate). If you wanted to use system python, deactivate the base environment (conda deactivate). If you have questions or difficulties, we will gladly help you

Sincerely

Mario S.