[phenixbb] Best practices for modified aminoacids

Morten Groftehauge mortengroftehauge.work at gmail.com
Tue Mar 5 06:16:29 PST 2013


I have an S-methylcysteine sulfoxide so I downloaded it from WebCSD from
the CCDC website. So far so good. Available in three formats but I wanted
it to work as a modified residue so I followed the advice here. Opened it
in PyMol, saved it as a pdb file and edited the atoms in a text editor to
fit with a normal residue. But phenix.elbow doesn't treat sulfur correctly.
The geometry is right but it adds an extra hydrogen to the sulfur and the
oxygen - they should have a double bond instead. If I run phenix.elbow
directly on the files downloaded from WebCSD I get the double bond but I
also get a flat system; as if my sulfur was a carbon.
Yes, I tried --opt.
Attached the best results.
My phenix version is 1299.

tl;dr phenix.elbow fails at parameterising DMSO.



On 29 July 2012 04:41, Paul Emsley <paul.emsley at bioch.ox.ac.uk> wrote:

>  On 27/07/12 13:43, Schubert, Carsten [JRDUS] wrote:
>  What are the current best practices for modified aminoacids? I have a
> peptide with and N-terminal Acetyl-proline which I am trying to model. The
> initial approach was to locate the aminoacid in the chemical components
> dictionary (N7P) and replace the residue in coot.
> do the restraints specify that N7P is a non-polymer (in which case coot
> will treat it as such) or as an L-peptide?
>   Unfortunately the link to the next residue is not recognized, so the
> residue is just floating about.
> Doesn't sound very much like how a L-peptide should behave to me...
> Paul.
> _______________________________________________
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> phenixbb at phenix-online.org
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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