[AMBER] MMGBSA error mitigation

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Sat, 13 Nov 2021 13:16:03 +0000

Hi everyone,

I am trying to compute the binding affinity of a ligand to a mark4kinase.
Input file is:

Input file for running PB and GB
   endframe=100, keep_files=2,
  igb=2, saltcon=0.100,

I have the complex_solvated files, the complex_dry prmtop , the receptor prmtop and the ligand.prmtop
The job submitted runs for about 2 hrs and then it shows a error and I am bit lost as I am unable to track down what is wrong with my setup?
All the _MMPBSA_ temp files get created and then my slurm.out file says this:
I see it says fatal error with the protein.prmtop I checked it 3 times it looks fine just the receptor and chloride ions are in the prmtop. I am not sure how to troubleshoot this.

Hostname = exp-1-26
Date = Fri Nov 12 14:14:29 PST 2021
Loading and checking parameter files for compatibility...
cpptraj found! Using /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/cpptraj
mmpbsa_py_energy found! Using /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/MMPBSA.py", line 100, in <module>
  File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 475, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/cpptraj failed with prmtop protein.prmtop!

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.


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Received on Sat Nov 13 2021 - 05:30:02 PST
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