Hi Amber community!
I am trying to run mmpbsa using pbsa=2 on 300 frames of the last 50ns of
trajectory but am continuously encountering problems. Your input is greatly
appreciated. My input file is below followed by the errow statement.
PBSA with PARSE RADII
&general
startframe=1, endframe=9999, interval=1, netcdf=1,
ligand_mask=":336-678", receptor_mask=":1-335",
use_sander=1,
/
&pb
inp=2, radiopt=1, istrng=0.100,
CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top!
calc.run(rank, stdout=stdout, stderr=stderr)
Error occured on rank 7.
Exiting. All files have been retained.
File
"/home/divi/gccamber/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/divi/gccamber/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top!
[cli_7]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
Error occured on rank 13.
Exiting. All files have been retained.
self.prmtop) + '\n\t'.join(error_list) + '\n')
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top!
--
Shenna Shearin
PhD candidate
Department of Computational Science & Engineering,
North Carolina A & T State University
Greensboro, NC 27411
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Received on Fri Aug 07 2015 - 18:00:02 PDT
