Re: AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands

From: Holger Gohlke <>
Date: Mon, 18 Aug 2003 08:50:49 -0700

> Hello AMBERs,
> I just wanted to ask whether it is possible to decompose energies to
> main-chain/side-chain contributions for non-amino acid ligands. If not, Is it
> planned for the future?
> All the best,
> Martin Lepsik

In mm_pbsa of amber7, energy decomposition also works for non-amino acid
ligands, i.e. you can obtain energy contributions for each residue
(where "residue" should be understood with respect to the parmtop file,
not just a protein). For non-amino acid residues, a
main-chain/side-chain split up of the contributions is not given.
Instead, all contributions are summed as "side-chain" contributions.

Best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla, CA 92037   USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
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Received on Mon Aug 18 2003 - 16:53:01 PDT
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