Re: [AMBER] Parameters for SulfoTyrosine

From: Brian Radak <radak004.umn.edu>
Date: Wed, 30 Jul 2014 11:08:31 -0400

Putting "sulfotyrosine molecular dynamics" into Google Scholar I find the
following paper:

Glover and Tracey, Structure, modelling, and molecular dynamics studies of
the inhibition of protein tyrosine phosphatase 1B by sulfotyrosine
peptides, *Biochemistry and Cell Biology*, *1999*, *77*, 469-486.

The literature it almost always a better place to start for such things
than the AMBER listserv.

Regards,
Brian

P.S. Sulfur in AMBER is probably best handled by GAFF, for which atom types
are either automatically assigned by Antechamber and/or easily confirmed by
looking at the parameter definitions. These are not always satisfying (for
example P-S bonds) and the Lennard-Jones parameters are probably not fully
optimized (they are the same in all cases).


On Wed, Jul 30, 2014 at 10:52 AM, Stephane Azoulay <s.azoulay.unistra.fr>
wrote:

> Dear Amber community,
>
> I need to do molecular dynamics simulations of a protein which contains
> sulfotyrosine residues.
> Does anyone has already done it before?
>
> At the moment, I am trying to create parameters for this residue but
> it's the first time i'm doing this.
> What is the correct amber atom type for the sulfur atom? S6, SY, ... ?
> What should be the atom types of oxygen atoms linked to the sulfur?
>
> Thank you for your help,
>
> St├ęphane
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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Received on Wed Jul 30 2014 - 08:30:02 PDT
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