[gmx-users] ATP+Mg

Алексей Раевский rayevsky85 at gmail.com
Sat Mar 19 02:01:41 CET 2011

I'm working with kinase with ATP in active site. ATP topology was created by
swissparam.ch server, as well as I'm working with charmm27 in gromacs 4.5.3.
Using superposition of the protein models I've found  coordinates for ions
which have to stabilize ATP (Mg2+). For this purpose we used MgCl in the
real experiments. I know, that Zn atoms in protein I can bind changing
protonation type of aminoacid CYS and HIS which formed 4 bonds with Zn. And
I need your help in this question! Of course I shouldn't create "bond" and
"angel" between etheric O and magnesium. May be I have to PULL this Mg2+
atoms? and if it is so - which PULLING method I need (distance or else)?

Thank you very much
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