Marc Charendoff wrote:
So sorry! You're absolutely right. Re the question on Zn 2+ I am asking
about the ffgmx forcefield.
I don't believe the answers to your questions are in the public domain, for
several reasons. First, ffgmx is an old, deprecated force field that is
somewhat of a hodge-podge of many different parameters (reference previous
discussions on the list). For any new simulation, I would strongly recommend a
more modern force field. Second, the official reference for the Gromos87 force
field (the backbone of ffgmx) is the Gromos87 user's manual, which one has to
pay a license fee to obtain.
Based on literature of more recent Gromos96 force field parameter sets (53a5 and
53a6), I would think that coordination geometry was not involved. Other details
are still sparing regarding ion parameterization, aside from a small section
describing repulsive terms between ions in the Gromos96 53a5/53a6 paper.
-Justin
Marc Charendoff wrote:
> Hello,
>
> I am curious - is there anyway to see what assumptions were
made when parameterizing the Zn 2+ ion? Was it tetrahedrally or
octahedrally coordinated? With waters only or with imidazoles? Do the
different force fields make different assumptions? Guidance appreciated.
Without even knowing the force field to which you were referring, we
can't say anything other than to refer you to the primary literature for
that force field.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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