AMBER Archive (2007)

Subject: AMBER: Problems with Carbohydrate Non-standard Residue

From: Moruz Luminita (moruzlumi_at_yahoo.com)
Date: Wed Sep 12 2007 - 05:30:09 CDT

Hello everyone,

I am trying to model a carbohydrate that contains a
Rhap4NAc residue using Glycam. Since I have just
started using Amber, I thought the safest way would be
to use the online tool available for building
carbohydrates
(http://www.glycam.com/CCRC/biombuilder/biomb_index.jsp).
Unfortunately it seems that Rhap4NAc is not included
in any library, as the sequence was not recognized by
this tool. Therefore I thought the easiest way to deal
with this problem would be to treat it as a
nonstandard residue and apply the same steps as
explained in Tutorial 4
(http://www.rosswalker.co.uk/tutorials/amber_workshop/).
First, when building the pdb file, I replaced Rhap4NAc
with a Rha, then I loaded the pdb file in xleap and I
added the NAc group by hand. Afterwards, following the
suggestions in the tutorial, I renamed the Rha4NAc
residue in the Pdb file and made a separate pdb that
contains only this residue. I loaded it as a separate
unit in xleap and I added the bonds by hand, but now I
got stuck because I dont know how to fill the atom
types. (for the charges I thought of using RESP)
Could somebody tell me whether this approach is ok or
maybe there is a better way to deal with this Rhap4NAC
residue? And can you point out some place where I can
get more information about atom types for
carbohydrates?
Any suggestion would be helpful to me, since though I
am studying Bioinformatics now, my background is
computer science and thus I face many problems when
dealing with chemistry issues.

Thank you in advance,
Mihaela

       
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