AMBER: Problems with Carbohydrate Non-standard Residue

From: Moruz Luminita <>
Date: Wed, 12 Sep 2007 03:30:09 -0700 (PDT)

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
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
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
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,

Pinpoint customers who are looking for what you sell.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Sep 16 2007 - 06:07:06 PDT
Custom Search