RE: AMBER: Problems with Carbohydrate Non-standard Residue

From: Irene Newhouse <einew.hotmail.com>
Date: Wed, 12 Sep 2007 06:58:17 -1000

You're on the right track. To fill in the atom types, look at other similar residues. For instance,
sialic acid [residue SA] and N-acetyl glucosamine [residue YB] both have Nac groups whose partial
charges & atom types you can "borrow" for Rhap4Nac. The idea is that the chemistry is mostly
quasi-local & a Nac group is a Nac group, is a Nac group. Etc.
 
Irene Newhouse
> Date: Wed, 12 Sep 2007 03:30:09 -0700> From: moruzlumi.yahoo.com> Subject: AMBER: Problems with Carbohydrate Non-standard Residue > To: amber.scripps.edu> > 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> > > > ____________________________________________________________________________________> Pinpoint customers who are looking for what you sell. > http://searchmarketing.yahoo.com/> -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to amber@scripps.edu> To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu
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Received on Sun Sep 16 2007 - 06:07:11 PDT
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