dear users of Amber
I am trying to perform a free energy calculation as follows:
MMGBSA-DECOM
&general
startframe=20000, endframe=25000, interval=1,
verbose=2, keep_files=2, debug_printlevel=2,
/
&gb
igb=2, saltcon=0.000
/
&pb
istrng=0.100, radiopt=1, inp=1,
/
&decomp
idecomp=2, dec_verbose=1, csv_format=0, print_res="1-940"
/
However I receive the following message, can someone help me?
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/chem/amber18/bin/sander
cpptraj found! Using /usr/local/chem/amber18/bin/cpptraj
Preparing trajectories for simulation...
5001 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/chem/amber18/bin/sander
calculating complex contribution...
calculating receptor contribution...
File "/usr/local/chem/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /usr/local/chem/amber18/bin/sander failed with prmtop
complex.prmtop!
Error occured on rank 5.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Mon Feb 01 2021 - 04:00:02 PST
