Dear all,
I have one question about MMPBSA.py.MPI. I am using MMPBSA to calculate
binding energy between receptor and ligand.
The serial version MMPBSA.py is working. But parallel MMPBSA.py.MPI (for a
test, I used 8 processor for 8 frames) is not working for PBSA (but it is
working for GBSA). The error message is:
Beginning PB calculations with
/cluster/apps/x86_64/packages/amber12/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError:
/cluster/apps/x86_64/packages/amber12/amber12/bin/mmpbsa_py_energy failed
with prmtop system.prmtop!
I have searched amber maillist and found 2 possible solutions:
1. set inp=1 and radiopt=0
2. remove the dec_verbose variable from the MMPBSA_pb.mdin
but Neither of them is working for my case. Because my system is huge, I
have to use parallel version of MMPBSA command. I am using Amber12.18 and
AmberTools 12.37. Anyone has solution for this problem?
Thanks,
Best regards,
zhongqiao Hu
Bioinformatics Institute, ASTAR, Singapore
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Received on Mon Feb 03 2014 - 01:00:02 PST
