Re: [AMBER] glycated residue parameter

From: Sangita Kachhap <>
Date: Mon, 04 Aug 2014 14:54:51 +0530


Is there any option other than Gaussian for geometry optimization for
this non-standard residue?


On 2014-08-04 1:05 pm, wrote:

> Hi!
> Remember that antechamber can only deal with whole molecules, not with fragments. If what you're parameterizing is a residue, I wouldn't really trust the results. Probably the easiest way would be to either follow the indications in the old non-standard residue tutorial, or define a non-standard atom for whatever position you have attached your glycan to, and then simply use glycam nomenclature + the bond command on x- or tleap to attach the glycan to that atom.
> Hopefully that helps,
> Manuel
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Sangita Kachhap
C/O Dr. Balvinder Singh
AMBER mailing list
Received on Mon Aug 04 2014 - 03:00:02 PDT
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