[AMBER] Issue with intramolecular pairwise-residue energy decomposition

From: <rohitarora10.gmail.com>
Date: Mon, 9 Sep 2013 09:33:23 +0200

Dear Amber users,

I am trying to calculate the intramolecular pairwise-residue energy
decomposition for a small protein. The protein is an apo monomer (no
ligand). I have tried the MMPBSA.py method as explained in the manual.
Since the system is not a complex, I used a single monomer for the complex
file with the command:

MMPBSA.py -O -i mmpbsa_decomp.in -cp receptor.top -y receptor.crd

In the output, the total energy for Res# n - Res# n is not null between
identical residues as I would be expected.

I tried also to create a 'complex' pdb by putting the same protein as both
receptor and ligand (superimposed) with exactly the same coordinates for
all the atoms. So I have 3 top files - com.top (2xMonomer), rec.top
(Monomer), lig.top (Monomer). In this case, the calculation exits with the
following error:
"Beginning GB calculations with /opt/amber12/bin/sander
  calculating complex contribution...
CalcError: /opt/amber12/bin/sander failed with prmtop com.top! "

So I would like to know if it is possible to calculate, using MMPBSA.py,
the intramolecular pairwise-residue energy decomposition for each
residue-pair for a protein which is not complexed with any ligand or
another protein.

Thank you
Best regards
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Received on Mon Sep 09 2013 - 01:00:02 PDT
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