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.
-Justin
Thank you very much
--
========================================
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
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