Re: [AMBER] phosphorylated cysteine

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 17 Jan 2011 12:02:11 +0100

Dear Zhongjie,

> I want to do the MD simulation which needs parameters for
> phosphorylated cysteine with AMBER Force Field used in Gromacs software.

You could use the R.E.D. Tools or R.E.D. Server for that.
See http://q4md-forcefieldtools.org

You could define 2 (or 3) building blocks such as the Cysteine
dipeptide & thio-phosphate derivative(s) and use inter-molecular
charge constraint(s) (INTER-MCC) during the fit to reconstruct your
phosphorylated cysteine.

Cysteine dipeptide + thio-phosphate derivative(s) -> phosphorylated
cysteine(s)

You could start by testing:

     R-SH + Me-S-PO3(2-) -> R-S-PO3(2-)
       <-------------------->
           INTER-MCC sets to zero
                       + Me-S-PO3H(-) -> R-S-PO3H(-)
       <-------------------->
           INTER-MCC sets to zero

To study the impact of the INTER-MCC(s) used R.E.D. Server includes by
now a statistics module.

You could follow the approach described .
http://q4md-forcefieldtools.org/REDDB/projects/F-72/
http://www.ncbi.nlm.nih.gov/pubmed/21192681
The molecules are different but a similar approach should work...

See Tutorials . http://q4md-forcefieldtools.org/Tutorial/
You could associate the approach defined . (for amino-acid fragments)
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
  & INTER-MCC as defined .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26

regards, Francois



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Received on Mon Jan 17 2011 - 03:30:04 PST