Hi Dmitry,
I've thought about this briefly myself. I'm not an expert, but I can't
think of any obvious problems with the link atom procedure. However, it
might be interesting to check exactly which MM dihedral terms are kept also
(e.g. C4' - C3' - C2' - C1'). Their could be energy conservation issues
somewhere in there from violation Newton's 3rd law.
What will almost definitely be problematic is the partial charges on the MM
atoms, since the ring is very unlikely to be partitioned into regions of
integer charge. I think the default is to take the excess charge, divide
it by the number of atoms, and reapportion it evenly amongst *all* MM atoms
(offhand I don't know what options are available for this). That seems
rather dubious to me, but it's a convenient automatic solution.
Personally, I would try to reassign the charges in the prmtop via some RESP
procedure with constraints, but I don't really know how one would do that.
What kind of molecule/fragment do you fit?
Hopefully Ross will chime in here with more answers than questions.
Regards,
Brian
On Fri, Jan 27, 2012 at 8:12 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> Dear Amber community!
>
> I want to split a cyclic molecule into quantum mechanics (QM) and
> molecular mechanics (MM) parts during QM/MM MD simulation (with the
> use of semiempirical methods incorporated into Amber10 Sander module)
> as depicted in the attached file. But I am not shure that such a
> partitioning is acceptable. Are there any known problems related to
> splitting a cycle into QM and MM regions?
>
> Thanks in advance and excuse me for this off-topic question!
>
> --
> Dmitry Nilov
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
> web: http://enzyme.fbb.msu.ru/
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Fri Jan 27 2012 - 08:00:02 PST
