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

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 19 13:27:43 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>
>     <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?

Whatever is necessary to properly produce the coordination complex.  Usually ATP 
should remain stably bound to most proteins, but metal ions can drift away.

> 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?

Either.  Fixed point charge models for metal binding sites are one significant 
limitation of molecular mechanics force fields.  There are significant inductive 
effects that are not accounted for.



> Sorry for I repeat the question


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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