AMBER Archive (2001)

Subject: ATP+Mg, P-tyrosine a P-threonine

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Wed Mar 14 2001 - 04:35:53 CST

Dear AMBER users,

i have two questions;
the first, i would like to simulate complex protein-MG-ATP where Mg is
hexacoordinated by 2oxygens from protein, 1oxygen from water molecule and
3 oxygens from ATP phosphates. Can i use AMBER parameters for Mg directly
and parametrize alone ATP--- ion? or have i to parametrize ATP together
with Mg++ ion as ATP-Mg complex? or ATP-MG-water molecule? or ...?

the second, Has anybody parametres (prep files and mod. ff params) for
ATP, ATP-MG and/or for phosphorylated tyrosine and threonine.

Thank you very much in advance,

        Michal Otyepka

      
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