Hi!<br>I'm working with kinase with ATP in active site. ATP topology was created by <a href="http://swissparam.ch">swissparam.ch</a> 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)?<br>
<br>Thank you very much<br>