ValueError: invalid literal for int() with base 10: '52A'

[Muhamad Alif Bin Che Nordin]

Hi everyone!

I think my issue at hand is somewhat similar to the other discussion

Error in running gmx_MMPBSA 31 Aug 2021

To get yourselves into perspective, I am simulating antibody (chain H & chain L, separately) and receptor (chain R) binding using Martini Coarse-Grained MD on GROMACS 2018 MD simulation system. Then i used performed resolution transformation using Backward to turn my biomolecules back to all-atomic.

For CGMD im using Martini FF. Backmapping was done using CHARMM36 FF. During insert membrane process of CGMD, periodic boundary condition type was set (cubic).

Prior to commencing gmx MMPBSA command, an index file was prepared by determining the atoms of VH, VL and Receptor from all-atomic complex TPR file. PBC was removed, and the biomolecules were centered and fitted.

The command gmx_MMPBSA perform to estimate MMPSA binding energy between groups VH-VL and receptor. The output is as below:

$ gmx_MMPBSA -O -i mmpbsa.in -cs mmpbsa.tpr -ci mmpbsa.ndx -cg 10 11 -ct mmpbsa_fit.xtc -cp topol.top
[INFO   ] Starting gmx_MMPBSA v1.5.0.3
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs mmpbsa.tpr -ci mmpbsa.ndx -cg 10 11 -ct mmpbsa_fit.xtc -cp topol.top

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/alifnordin/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/alifnordin/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/alifnordin/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/alifnordin/anaconda3/envs/gmxMMPBSA/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   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 10_11 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 10 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 11 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 10, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 415, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 685, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 311, in read
    molecule.add_atom(*self._parse_atoms(line, params))
  File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/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: '52A'
Exiting. All files have been retained.

FYI, the software was properly installed and gmx_MMPBSA_test was performed without any error.

Can anyone please help me with this error? Thanks'

Alif Nordin

[Mario Sergio Valdes]

Hi and welcome. 

Thank you for the detailed explanation of the error, this helps to identify it more quickly.

If you followed the installation steps described in the documentation, then this should not happen, since the ParmEd update includes this fix. One of the most common problems is that you have AmberTools compiled and source amber.sh in your .barshrc. This would override the PYTHONPATH variable causing gmx_MMPBSA to use the ParmEd installed in AmberTools instead of the one installed in their conda environment. You can check if the PYTHONPATH is assigned (echo $PYTHONPATH). If it has a value, unset PYTHONPATH (only affects the current section, it is reset as soon as you open a new terminal) and test if it works for you.
In case this is the problem, you can create an alias to simplify the process
alias activategmxMMPBSA="unset PYTHONPATH; conda activate gmxMMPBSA".

Let me know if the problem is solved.

Mario S.

[Muhamad Alif Bin Che Nordin]

Thank you for your response.

Unfortunately upon submitting echo pythonpath, it didn't produce any value.

However, I did perform pythonpath unset as recommended but still produce the same outcome.

Do you think this has anything to do with submitting multiple chains of biomolecules (i.e., VH, VL and R) for gmx_MMPBSA?

[Muhamad Alif Bin Che Nordin]

to add more points:

I did try run a sample from my colleague: we apply the same method, with the only notable difference is he is using a single-chain Fv against a receptor compared to mine (VH, VL against receptor).

It worked on the sample, but not mine.

[Mario Sergio Valdes]

Show me the current ParmEd used by gmx_MMPBSA as follows

python 

import parmed

parmed.__file__

[Mario Sergio Valdes]

Please try installing the updated ParmEd version as follow:

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

Make sure to activate the gmxMMPBSA environment first
 

[Muhamad Alif Bin Che Nordin]

Thank you for the points.

I managed to run the command, however, it gave the following output:

File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA, line 10, in <module> sys.exit(gmxmmpbsa())
File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 113, GMXMMPBSA app.write_final outputs()
File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 601, in write_final_outputs write outputs(self)

File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/output_file.py", line 339, in

final_output.writeline(sys_norm.report_inconsistency())

File "/home/alifnordin/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/output_file.py", line 668, in writeline self.write(line + ls)

TypeError: unsupported operand type(s) for: 'NoneType' and 'str'

Exiting. All files have been retained.

Appreciate your help on this. thanks

[marioe911116]

this error happens when there are inconsistencies in the internal potentials. It has been corrected already... please update gmx_MMPBSA as follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

you could also check this thread for more details:

https://groups.google.com/g/gmx_mmpbsa/c/L5Tpv0AWRK0

please, let us know if that solves the problem...

[Muhamad Alif Bin Che Nordin]

thank you your advise. i think it worked!

thank you everyone