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

From: caobb0214 <>
Date: Tue, 27 Mar 2012 09:56:22 +0800 (CST)

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
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Received on Mon Mar 26 2012 - 19:00:03 PDT
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