Hello,
I am calculating entropy using nmode and I am getting the following error
with com.prmtop. I have used the same file for MMPBSA analysis and it
worked fine. But, It is showing errors with entropy calculation.
File "/home/apps/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 323, in run
Calculation.run(self, rank, stdout=self.output % rank)
File
"/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/apps/amber18/bin/mmpbsa_py_nabnmode failed with prmtop
com.prmtop!
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
FATAL: allocation failure in vector()
FATAL: allocation failure in vector()
FATAL: allocation failure in vector()
FATAL: allocation failure in vector()
Here is the input file-
Input file for running entropy calculations using NMode
&general
endframe=20000, keep_files=0,
verbose=1, use_sander=1
/
&nmode
nmstartframe=10200, nmendframe=20000,
nminterval=200,
maxcyc=50000, drms=0.0001,
/
Kindly help me in resolving the issue.
Thank you
--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Sun Apr 07 2024 - 02:30:02 PDT
