Hi! 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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