AMBER Archive (2007)

Subject: Re: AMBER: phosphorylation

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Dec 06 2007 - 14:07:57 CST

Quoting bosco <apposite_at_gmail.com>:

> I'm trying to work out how to add an aspartyl-phosphate to my protein in a
> simulation.

You might be interested in reading:
N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht,
J. Mol. Model. 2006, 12, 281-289.
AMBER force field parameters for phosphorylated amino acids in
different protonation states: phosphoserine, phosphothreonine,
phosphotyrosine and phosphohistidine
See http://pharmacy.man.ac.uk/amber/

Concerning how building new residue fragments, you could look at
R.E.DD.B. where different central, N-terminal & C-terminal fragments
are available.

regards, Francois

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