Dear Andreas! Thank you for your reply!
Do you mean the following variant to be better:
5) CH3-[-CO-NH-CHR-]-CO-NH-CH3 ?
On Thu, Feb 27, 2014 at 2:44 AM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> Dear Dmitry,
>
> In QM/MM simulations it is in not a good idea to cut an amide bond. With
> link atom methods the best choice for the QM/MM boundary is to be at C-C
> single bonds. Highly polar bonds or bonds with (partial) double bond
> character are not good choices. The QM/MM partitioning in the paper you are
> referring was used to test energy conservation of the implementation, that
> is, to test whether the implementation is correct - nothing more. Thus,
> your variants 1) to 3) are not good choices. Try to cut C-C bonds.
>
> All the best,
> Andy
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
> On Feb 26, 2014, at 6:17 AM, Dmitry Nilov wrote:
>
> > Dear Amber community!
> >
> > I want to include the backbone of a non-terminal residue into QM part
> > during QM/MM simulation (Amber 10, RM1 Hamiltonian) of a protein. I
> wonder
> > what QM and MM partitioning is appropriate in this case? In the Ross
> > Walker's article (Walker RC, Crowley MF, Case DA. The implementation of a
> > fast and accurate QM/MM potential method in Amber. J Comput Chem. 2008,
> 29,
> > 1019-1031) I've found the following variant of QM-MM boundaries (in
> alanine
> > dipeptide):
> > 1) CH3-CO-[-NH-CHR-CO-NH-]-CH3, where the boundaries are "[" and "]".
> >
> > But is this the best partitioning? Why is it better than the following
> > variants?:
> > 2) CH3-CO-[-NH-CHR-CO-]-NH-CH3
> > 3) CH3-[-CO-NH-CHR-CO-]-NH-CH3
> > 4) CH3-[-CO-NH-CHR-CO-NH-]-CH3
> >
> > Thanks in advance! Any comments will be appreciated!
> >
> > --
> > Dmitry Nilov
> > Faculty of Bioengineering and Bioinformatics,
> > Lomonosov Moscow State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Thu Feb 27 2014 - 00:30:03 PST
