Dear Team,
I am trying to run some MMGBSA calculations on simulations of a protein-protein complex. I keep encountering an error only when I include the entropy term in the &general namelist. My input file is shown below:
&general
startframe=2000, verbose=1, keep_files=2, entropy=1
/
&gb
igb=2, saltcon=0.150
/
&decomp
idecomp=2, print_res="28-37, 45-61, 72-77, 97-110, 151-161, 174-178, 216-225, 235-238, 252-265, 303-314",
dec_verbose=1
/
I am calling from the command line using the following script
mpirun MMPBSA.py.MPI -O -i 429_MMPBSA.in \
-cp 429_complex.top -rp 429_receptor.top -lp 429_ligand.top \
-y 429_nowat.md9.x -o 429_MMPBSA_energy.dat \
-do 429_MMPBSA_decomp.dat -eo 429_time.csv
If entropy is set to 0, the MMGBSA completes with no errors. However, when entropy is set to 1, I get variations on the following error:
Error: PDB _MMPBSA_avgcomplex.pdb: No frames read. atom=456 expected 8929.
Error: Could not set up '_MMPBSA_avgcomplex.pdb' for reading.
Error: DataSet_Coords_REF: Could not set up trajectory.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
File "/opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/bin/MMPBSA.py.MPI", line 101, in <module>
app.run_mmpbsa() # for membrane runs by automatically setting the membrane thickness and location.
^^^^^^^^^^^^^^^^
File "/opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/lib/python3.11/site-packages/MMPBSA_mods/main.py", line 225, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/lib/python3.11/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/lib/python3.11/site-packages/MMPBSA_mods/calculation.py", line 419, in run
Calculation.run(self, rank, stdout=self.output)
File "/opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/lib/python3.11/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /opt/scp/apps/gen-2023a/software/Amber/24.2-foss-2023a-AmberTools-24.6-CUDA-12.1.1/bin/cpptraj failed with prmtop 429_complex.top!
Error occurred on rank 248.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
Variations on the error message are primarily in the first line, where the atom= can seem to be any random number. I have checked the _MMPBSA_avgcomplex.pdb file and visualised it in PyMol. Everything seems OK and I can see the required numbers of atoms. Simulations run fine in VMD. Trajectories have been prepared in cpptraj using autoimage and stripping :WAT and :NA. Top files for MMGBSA have been generated using ante-MMPBSA.
Any tips on how I can get around this error? Like I say I've got the calculations for the MMGBSA but would like to get some entropy corrections.
Thanks in advance
Mark Waterhouse
Postdoctoral Fellow
_____________________________________________________________________
AstraZeneca
R&D Biologics Engineering
Discovery Centre (DISC), Cambridge Biomedical Campus, 1 Francis Crick Avenu, Cambridge, CB2 0AA
Mark.waterhouse.astrazeneca.com<mailto:Mark.waterhouse.astrazeneca.com>
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Received on Wed Apr 16 2025 - 06:30:02 PDT
