[AMBER] MMGBSA CalcError: mmpbsa_py_energy failed with prmtop

From: Maschietto, Federica <federica.maschietto.yale.edu>
Date: Wed, 28 Jul 2021 17:46:46 +0000

Dear Amber users,
I am trying to run mmgbsa calculations on a protein-protein complex however, I am hitting an error: a problem occurs when reading the dried_complex topology.

  File "/gpfs/loomis/project/batista/fm388/amber20/bin/MMPBSA.py", line 100, in <module>
  File "/gpfs/loomis/project/batista/fm388/amber20/lib/python3.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/gpfs/loomis/project/batista/fm388/amber20/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/gpfs/loomis/project/batista/fm388/amber20/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 157, in run
CalcError: /gpfs/loomis/project/batista/fm388/amber20/bin/mmpbsa_py_energy failed with prmtop C1_dry.prmtop!
Exiting. All files have been retained.

The _MMPBSA_complex_gb.mdout.0 output file shows the following error:

Reading parm file (C1_dry.prmtop)
mm_options: e_debug=2
mm_options: gb=8
mm_options: rgbmax=25.000000
mm_options: gbsa=0
mm_options: surften=0.007200
mm_options: cut=999.000000
mm_options: epsext=78.300000
mm_options: kappa=0.000000
Error: gb>0 is incompatible with periodic boundary conditions.
Error: To use this method set IFBOX in the PRMTOP file to 0.
Error: See http://ambermd.org/formats.html

Should I change any lines in the C1_dry.prmtop file?
I generate this topology by using the following cpptraj command:

parm C1_solv.prmtop
parmstrip :WAT|:Na*|:Cl*
parmwrite out C1_dry.prmtop

I don't see any obvious error in the generated topology: the file contains the expected number of residues (and no solvent molecules or ions). Besides, VMD loads the file without problem. I read in a previous thread on the same topic, that specifying the strip_mask, receptor_mask and ligand_mask explicitly in the mmgbsa input file might solve the problem. However that did not solve the issue.
The full input file I am using is the following:

mmgbsa test
 startframe=1, endframe=2, verbose=6,
 strip_mask=':WAT|:Na*', receptor_mask=":1-3477", ligand_mask=":3478-6366",

I am running the calculation using the following command
MMPBSA.py -O -i mmgbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp C1_solv.prmtop -cp C1_dry.prmtop -rp receptor.prmtop -lp ligand.prmtop -y heat_2.nc > progress.log 2>&1

Besides, I checked that receptor.prmtop and ligand.prmtop sum up to the the number of atoms contained in C1_dry.prmtop and that the number is consistent with that in C1_solv.prmtop. Any suggestion on what might be the origin of the problem would be greatly appreciated.

Thank you in advance,
Federica Maschietto
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Received on Wed Jul 28 2021 - 11:00:02 PDT
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