My script is this
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp serotonin_Mark4.prmtop -cp serotonin_Mark4_gas.prmtop -rp protein.prmtop -lp ligand.prmtop -y ./run1/serotonin_mark4_production4A.nc
mmpbsa.in looks like this:
Input file for running PB and GB
&general
endframe=2000, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
Error I get in my slurm.out is as follows:
Hostname = exp-2-13
Date = Fri Nov 12 04:14:58 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...
1250 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...
File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
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 156, 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/mmpbsa_py_energy failed with prmtop serotonin_Mark4_gas.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.
/cm/local/apps/slurm/var/spool/job7028864/slurm_script: line 38: /home/debarati: Is a directory
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Received on Fri Nov 12 2021 - 04:30:03 PST
