gbnsr6 failed with prmtop -i

[Fernando Gutierrez]

Dear gmx_MMPBSA team,

I am writing to request assistance with an issue I encountered while running gmx_MMPBSA to calculate dH contribution on an insulin-receptor complex with the GBNSR6 mode. The program reported the following error: 

[INFO   ] 1000 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 1 CPUs...
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GBNSR6 calculations with /home/fernando/miniconda3/envs/gmxMMPBSA/bin/gbnsr6
[INFO   ]   calculating complex contribution...
[INFO   ]     calculating MM...
            100%|##########################################################################################################################| 1000/1000 [elapsed: 48:40 remaining: 00:00]
[INFO   ]     calculating GB...
              0%|                                                                                                                                 | 0/1000 [elapsed: 00:00 remaining: ?]  File "/home/fernando/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==0+unknown', 'console_scripts', 'gmx_MMPBSA')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fernando/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/gmx_MMPBSA-0+unknown-py3.11.egg/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/fernando/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/gmx_MMPBSA-0+unknown-py3.11.egg/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/fernando/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/gmx_MMPBSA-0+unknown-py3.11.egg/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/fernando/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/gmx_MMPBSA-0+unknown-py3.11.egg/GMXMMPBSA/calculation.py", line 198, in run
    raise CalcError(f'{command_args[0]} failed with prmtop {command_args[1]}!')
CalcError: /home/fernando/miniconda3/envs/gmxMMPBSA/bin/gbnsr6 failed with prmtop -i!
Exiting. All files have been retained.
real 49m29,168s
user 52m32,736s
sys 0m3,135s

Could you please advise on what might be causing this issue?

Thank you very much for your help.

Best regards,

Fernando

--

Fernando Gutiérrez

Bioinformatics Engineer Leader

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[mariosergi...@gmail.com]

Can you send me your files so I can reproduce the error?

[mariosergi...@gmail.com]

I haven't identified the error; it seems it's not happy with the dihedrals. I've run several tests over the past few days.
- I checked to see if it was due to the size, but it doesn't seem to be. I tested a much larger system and it works.
- I tried selecting fragments of your system as the receiver, and it works strangely. For example, if the receiver is defined as ri 52-99, it works fine, but if I select ri 52-100, it fails. If I select ri 103-152, it works, but ri 103-153 doesn't. Now, the only notable thing about this is that residues 100, 102, and 153 are ILE, ILE, and ASN. Both have dihedrals modified by the amber99-ILDN force field, and coincidentally, the error message mentions it (rdparm: a parameter array overflowed (e.g., the table of dihedral params)).
- I tried charmmff and it works, but it also failed with a system prepared with amber99SB. I couldn't test it with amber14SB or amber19SB, but I assume it will fail since they are technically similar to amber99SB.
Honestly, I have no idea why it fails, but I assume it's an internal problem with the gbnsr6 program. In your case, I'm not sure it will contribute much, given that the only improvement it's noticed compared to conventional GB is for small molecules. Anyway, I'll try to identify the problem, although it will take time.