AMBER Archive (2009)

Subject: Re: [AMBER] Saccharides chains termini

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jun 30 2009 - 10:47:04 CDT

Dear Sergey,

> 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?

You might be interested in comparing the GLYCAM approach & that presented
@ http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
   http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
This might help you in particular if you are interested in building
new monosaccharide fragments, or if you are interested in studying new
oligosaccharides.

The corresponding project is also available in R.E.DD.B. as the project F-72:
http://q4md-forcefieldtools.org/REDDB/projects/F-71/. Similar projects
should show up in R.E.DD.B. pretty soon.

If you compare the GLYCAM approach & what we did in this work the
position of the inter-unit glycosidic oxygen differs: The key question
here is where goes this inter-glycosidic oxygen...

regards, Francois

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