Antônio Pedro Lemos de Mesquita
Mar 20, 2025, 3:23:02 PMMar 20
to gmx_MMPBSA
Hello everyone, hope you guys are doing just fine. I am trying to perform a PB calculation for a system (protein + ligand + FAD). I am facing this error. Can anyone help me with this? Thank you very much!
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
^^^^^^^^^^^
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/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/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
tops = self.gmxtop2prmtop()
^^^^^^^^^^^^^^^^^^^^
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 566, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 853, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(temp_top.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 346, in __init__
self.read(fname, defines, parametrize)
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 413, in read
nbe, nbet = self._parse_pairs(line, exc_types, molecule.atoms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/antonio.mesquita/miniconda3/envs/gmxMMPBSA2/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py", line 634, in _parse_pairs
sig = float(words[3]) * 2**(1/6)
^^^^^^^^^^^^^^^
ValueError: could not convert string to float: 'C1'
Exiting. All files have been retained.
mariosergi...@gmail.com
Mar 20, 2025, 3:26:15 PMMar 20
to gmx_MMPBSA
Please, send me the original top+itp files and the temp topology that is generated during the calculation
mariosergi...@gmail.com
Mar 20, 2025, 5:30:51 PMMar 20
to gmx_MMPBSA
The problem is the [ pairs ] section in the ligand itp (ligand_GMX_OPLS.itp) doesn't have the atom names pairs commented. This section accepts multiple numeric columns but no strings. So, ParmEd tries to convert this text into a float number.
To solve the problem, you can add the ";" character before the text, for example
To solve the problem, you can add the ";" character before the text, for example
[line 101] 1 4 1 ; C1 - C4
or remove it
[line 101] 1 4 1
from the lines 101 to 167. I recommend using a text-column editor like Kate to change all at the same time
Antônio Pedro Lemos de Mesquita
Mar 20, 2025, 6:51:27 PMMar 20
to gmx_MMPBSA
I have no words to thank you for the quick and kind help! The problem was completely resolved. When I perform the OPLS parametrization of the ligand with ACPYPE, the topology file always comes with extra comments (;) that I need to remove so that GROMACS can read it. This time, I ended up removing more ; than necessary. I think I would never have been able to detect this fault on my own in time. Once again, I am immensely grateful for your assistance and for developing such a good and accessible software like gmx_MMPBSA. Greetings from Brasil!
mariosergi...@gmail.com
Mar 20, 2025, 6:54:52 PMMar 20
to gmx_MMPBSA
I am glad to help you... I just have the experience of several years looking at ParmEd code, :)
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