[AMBER] MMPBSA.py problem

From: Debodyuti Dutta <dutta.debodyuti.gmail.com>
Date: Tue, 4 Aug 2015 15:46:45 +0530

hello Amber users,

I am facing a strange problem in MM-PBSA and I would like to know if there
is any solution to it or
someone else is also facing the same.

In MM-PBSA we use the trajectory protein-ligand trajectory. It write 3
output files, namely, _MMPBSA_complex_pb.mdout.0,
_MMPBSA_receptor_pb.mdout.0, _MMPBSA_ligand_pb.mdout.0. Problem is that the
calculation is going on well if there is only 5 frames and the program is
writing the .dat files at the end of the calculation; but if there is ,lets
say, 5000 frames the calculation finishes after writing full
_MMPBSA_complex_pb.mdout.0 and not writing the other mdout files. There is
no error message of any kind. Although all 3 sets of mdcrd.0, pdb, inpcrd
and mdin files are generated by cpptraj before the calculations go through
Sander. I am using amber14.

any help will be appreciated. thanks in advance.

*Debodyuti Dutta*
Research Scholar
Indian Institute of Technology Kharagpur
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Received on Tue Aug 04 2015 - 03:30:02 PDT
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