Re: [AMBER] Including amino acid backbone into QM part during QM/MM

From: Andreas Goetz <agoetz.sdsc.edu>
Date: Wed, 26 Feb 2014 14:44:16 -0800

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
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Received on Wed Feb 26 2014 - 15:00:03 PST
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