[AMBER] Entropy calculation using nmode fails

From: Neha Rana <nrana.purdue.edu>
Date: Sun, 28 Sep 2014 10:35:27 -0400 (EDT)

I've been trying to calculate entropy of complexes of same protein - different ligands using nmode interface in MMPBSA.py . This is the input file I'm using,
 endframe=4800, keep_files=2,
 nmstartframe=1, nmendframe=4800,
 nminterval=100, nmode_igb=1, nmode_istrng=0.1

I'm also running it in parallel using MMPBSA.py.MPI and assigning the process 48 processors. I use all the flags, -sp , -cp, -rp, -lp and -y . But I'm constantly getting this error
CalcError: /apps/rhel6/amber/amber12/bin/mmpbsa_py_nabnmode failed with prmtop complex.prmtop!
I'm observing this error with all the ligands.

However, with one ligand when I use only first 32 frames of its trajectory and put the nminterval=1, it runs just fine. Though the vibrational entropies of complex and ligand are zero. And this is my second concern.

One thing I noticed was, the first and second snapshot of complex, receptor and ligand had two sets of coordinates in their respective _MMPBSA_complex(receptor/ligand)_nm.mdcrd.0 and _MMPBSA_complex(recpetor/ligand)_nm.mdcrd.1 files. I'm not sure if this is normal or affects my case in any manner.

Any help would be highly appreciated.
Thanks a lot!
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Received on Sun Sep 28 2014 - 08:00:02 PDT
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