Jason is correct- this is what is happening.
On Mar 27, 2012 12:53 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> 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.
>
> HTH,
> Jason
>
>
> On Mar 26, 2012, at 9:56 PM, caobb0214 <caobb0214.163.com> 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" <carlos.simmerling.gmail.com>
> wrote:
> >> Probably the additional C alpha hydrogen
> >> On Mar 26, 2012 9:05 PM, "caobb0214" <caobb0214.163.com> wrote:
> >>
> >>> dear all,
> >>> I did a per-residue decompostion with mm_pbsa.pl 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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> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Mar 27 2012 - 03:30:03 PDT
