[gmx-users] ATP+Mg

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 19 02:05:10 CET 2011

Алексей Раевский wrote:
> Hi!
> I'm working with kinase with ATP in active site. ATP topology was 
> created by swissparam.ch <http://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)?

I don't see how pulling is relevant here.  You could use it to enforce a 
restraint, but it's not necessary.  Distance restraints or type 6 bonds are 
probably more useful and straightforward.  You do certainly have the 
complication of whether or not the force field's charges for the amino acids are 
correct, which most likely they aren't, as most QM/MM studies would indicate.


> Thank you very much


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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