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.
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
-Justin
Sorry for I repeat the question
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
