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
*---------------------------------------------[*]-*
| Department of Inorganic and Physical Chemistry |
| Palacky University |
| tr. Svobody 26, 771 46 Olomouc, Czech Republic |
| |
|ph. +420 68 5222451 (+396) fax +420 68 522 5737|
| fax +420 68 563 4420|
|
http://aix.upol.cz/~otyepka |
|
http://www.upol.cz/kafch |
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Received on Wed Mar 14 2001 - 02:35:53 PST
