[AMBER] MM energy contributions of atoms in a molecule

From: Jas Kalayan <jas.kalayan.manchester.ac.uk>
Date: Mon, 27 Feb 2017 16:52:51 +0000

Dear Amber members,

Is it possible to determine just the MM part of the MMPBSA calculation of free energy? I wanted to determine only the MM energy contribution of each atom of a molecule in a vacuum using Amber 14.

>From per-residue decomposition, I can see that the .mdout.0 files break down energies of each side-chain and backbone for each frame into internal, vdw, eel, pol and sas. But I would have thought the internal, vdw and eel energies per residue were determined from the sum of all atoms in the residue. Would this also be the case for all atoms in the molecule summed to give the energy of the whole molecule? If so would it be possible to effectively go back a step and extract internal, vdw and eel energies for each atom?

Kind Regards,

AMBER mailing list
Received on Mon Feb 27 2017 - 09:00:02 PST
Custom Search