AMBER Archive (2009)

Subject: Re: [AMBER] Saccharides chains termini

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Tue Jun 30 2009 - 09:57:46 CDT

Hi Sergey,

        Much of this is explained in the Amber Toolkit manual. Terminal sugars are
noted by 0 in their three letter residue abbreviation (eg. 0GA, 0LB, 0XB,
0gA). Section 3.5 of the manual will show you a step-by-step procedure to
build a oligosaccharide that is capped with an -OH or -OCH3 group. You may
also want to look at the glycam website, where you can use an online tool to
generate oligosaccharides (http://glycam.ccrc.uga.edu/). The partial atomic
charges have already been developed for most carbohydrates, and are available
in the prep file library or from the glycam website.

Cheers,
Karl

On Tuesday 30 June 2009 16:32, Sergey Samsonov wrote:
> Hi AMBERs,
>
> I have the following question: when one creates a chain made up of
> saccharide monomers, it is common that the terminal residue has 0 as a
> first character in residue identifier, meaning that there is no more
> open valences to continue the chain. What is about another terminus of a
> saccharide chain? Though, for example, sequence {4GB 0GB} yields a
> structure with a possibility to create the topology and coordinates
> files without problems, there is C1 atom in the residue 4GB, which is
> connected to O, C2 and a hydrogen (only three atoms, while C1 is
> sp3-hybridized). Chemically it would be logical to add OH-group to this
> C1-atom. Do you think it would be the proper way to proceed? And what
> charges should I use then for the atoms C1, corresponding oxygen and
> hydrogen of OH-group?
>
> Thank you very much and best regards,
>
> Sergey
>
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