AMBER Archive (2009)

Subject: Re: [AMBER] Saccharides chains termini

From: Lachele Foley (Lists) (
Date: Tue Jun 30 2009 - 09:46:09 CDT

Hi, Sergey!

In order to facilitate making complex oligosaccharides, the OH is left
out of the residues and must be included explicitly. The residue name
(for historical reasons) is ROH. So, to make the chain you have in
mind, you would use

m = sequence { ROH 4GB 0GB }

Other terminal residues are available, notably OME (O-methyl), and TBT

You can also terminate the other end with an anomeric-carbon to
anomeric-carbon connection, for example:

m = sequence { 1GB 4GB 0GB }

Let me know if you have other questions.

:-) Lachele

On Tue, Jun 30, 2009 at 10:32 AM, 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
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA

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