Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion

From: Jason Swails <>
Date: Tue, 27 Mar 2012 00:52:10 -0400

My suggestion is to not read too much into the sidechain/backbone distinction in this case unless it's particularly important. The distinction is hard-coded into sander based on atom names, and is specific to atom names in proteins and nucleic acids.

Therefore, one (or maybe both, I haven't checked) of the alpha-carbon hydrogen atoms is not tagged as a backbone atom because it isn't in the list of atom names that sander recognizes.

There is no complicated algorithm based on chemical insight, just a list of atom names conforming to a convention.

Indeed, from an implementation standpoint, it's easier to think of glycine as having a H-atom side chain, since then it doesn't have to be special-cased. That's probably what happened here.


On Mar 26, 2012, at 9:56 PM, caobb0214 <> wrote:

> professor carlos simmerling,
> thank you very much for your reply. but glycine residue has two alfa hydrogens which are chemically identical. I am wondering whether mmgbsa decomp algorithm can discriminately recognise them with respect to backone and sidechain. treat both of them as sidechain atoms? or one backbone atom and one sidechain atom.
> At 2012-03-27 09:08:33,"Carlos Simmerling" <> wrote:
>> Probably the additional C alpha hydrogen
>> On Mar 26, 2012 9:05 PM, "caobb0214" <> wrote:
>>> dear all,
>>> I did a per-residue decompostion with in amber9. The total
>>> contribution from each residue to overall delta binding free energies
>>> seemed to be fine. However, when I chekced the backone and sidechain
>>> energy decomposition for each residue I found that one glycine residue had
>>> a non-zero side chain contribution (about -0.1kcal). Supposedly, the
>>> residue of glycine has no sidechain, thus its sidechain contribution should
>>> be zero. Can anybody give me some hints about this inconsistency of glycine
>>> sidechain contribution.
>>> thanks
>>> _______________________________________________
>>> AMBER mailing list
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Mar 26 2012 - 22:00:02 PDT
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