Re: [AMBER] Modified Cysteine

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 01 Oct 2013 17:17:42 +0200

Dear Devlina,

> I need to work with a protein with two S-Hydroxy Cysteine residues (CSO) ,
> how do I create a topology file for such a structure? Any help would be
> greatly appreciated.

I looked at http://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:41710

I think you need to find out what is the PKa value for this sulfenic
acid group
   http://en.wikipedia.org/wiki/Sulfenic_acid
I do not know if you need to consider the sulfenate:
http://www.ncbi.nlm.nih.gov/pubmed/11885266
or the sulfoxyde (which can be potentially asymmetric)...

then, you could use R.E.D. Server
see http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
  vs http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25

You could send a private assistance to request that the data generated
by R.E.D. Server/R.E.D. IV are post-processed by using R.E.D. Python
for atom typing... You will have to parameterize the sulfenic_acid
and/or sulfenate functions as well.

regards, Francois



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Received on Tue Oct 01 2013 - 08:30:06 PDT