Dear AMBER users and developer team,
I am trying to calculate the entropy of an RNA-protein complex using nmode.
But I am getting following error.
-----------------------------------
FATAL: allocation failure in vector()
File "/home/parimal1/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
app.run_mmpbsa()
File
"/home/parimal1/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/parimal1/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py"
, line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/parimal1/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py"
, line 323, in run
Calculation.run(self, rank, stdout=self.output % rank)
File
"/home/parimal1/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py"
, line 157, in run
self.prmtop))
CalcError: /home/parimal1/Software/amber18/bin/mmpbsa_py_nabnmode failed
with prmtop com_0W.prm
top!
Error occured on rank 11.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 11 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.
--------------------------------------------------------------------------
The same trajectory and topology, I used in my previous MMPBSA analysis. I
also try this nmode analysis with lesser number frame, but I get the same
error after certain number of steps. I am not able to understand the reason
of such error.
Please suggest me any solution to solve this error.
--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Sun Jun 30 2019 - 07:30:02 PDT
