[gmx-users] Re: gmx-users Digest, Vol 83, Issue 130

Алексей Раевский rayevsky85 at gmail.com
Sat Mar 19 08:11:36 CET 2011

> > 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.
> -Justin
> > Thank you very much

Thank you for a reply )))

First of all I've understood that Pulling is a bad idea. I tried to apply
several manuals, including this one
http://www.gromacs.org/Documentation/How-tos/Distance_Restraints. But what
about typing of 6 bonds? Bonds between ATP and Mg, Mg aminoacids?
This part of your message is unclear "whether or not the force field's
charges for the amino acids are correct, which most likely they aren't" what
aa did you mean, those I described with Zn binding or supposed Mg binding?
Sorry for I repeat the question
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