Value error during MMPBSA Calculation

Sarthak Trivedi SVNIT

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Dec 28, 2022, 11:25:42 AM12/28/22

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Respected Seniors/fellows,

I have received an error in both serial and parallel run in MMPBSA calcualtions. I request you to please look into the matter and guide me to proceed further. I actually checked on internet to solve this value error but the solution was not specific.

File "/home/drr-18/miniconda3/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
tops = self.gmxtop2prmtop()
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 338, in read
self._parse_dihedrals(line, dihedral_types, proper_multiterm_dihedrals,
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 590, in _parse_dihedrals
i, j, k, l = [int(x)-1 for x in words[:4]]
File "/home/drr-18/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 590, in <listcomp>
i, j, k, l = [int(x)-1 for x in words[:4]]
ValueError: invalid literal for int() with base 10: '#ifdef'
Exiting. All files have been retained.

Thank you so much for the wonderful support from gmx_MMPBSA team.

Regards,

Sarthak Trivedi.

Screenshot from 2022-12-28 21-29-38.png

Mario Sergio Valdes

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Dec 28, 2022, 12:41:37 PM12/28/22

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This error is because your topology seems to have problems. Send me the topology (*.top + *.itp + charmm folder if exists) to check it

Sarthak Trivedi SVNIT

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Dec 29, 2022, 2:30:04 AM12/29/22

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Here, i am attaching topol.top file, posre.itp, posre_unl.itp, charmm folder (ions.itp included).

Please have a look into it. Feel free for other files needed.

Regards,

Sarthak Trivedi

posre_unl.itp

posre.itp

topol.top

charmm36-jul2022.ff.zip

Mario Sergio Valdes

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Dec 29, 2022, 9:52:43 AM12/29/22

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Please, attach the unl related files (*.itp, *.prm, etc.)

Sarthak Trivedi SVNIT

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Dec 29, 2022, 10:50:01 AM12/29/22

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Please find all attachments related to UNL.

Thank you so much for the help

unl.top

unl.itp

unl.prm

UNL.str

unl_ini.pdb

posre_unl.itp

unl.gro

index_unl.ndx

Mario Sergio Valdes

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Dec 29, 2022, 12:52:36 PM12/29/22

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ParmEd seems to have a problem with whitespace in front of statements. In your case, the problem is in lines 60245-60248. Make sure that all definitions (# statements) are at the beginning of the line and do not contain spaces before

Mario S.

Sarthak Trivedi SVNIT

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Dec 29, 2022, 1:16:50 PM12/29/22

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Thank you so much. I can't say in words how much time you have saved for me. Thank you so much again. I spent a lot of time on this.

Regards,

Sarthak Trivedi.

Mario Sergio Valdes

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Dec 29, 2022, 1:33:46 PM12/29/22

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Don't worry, I'm happy to help you. Any other problem do not hesitate to contact us

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