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 - 06:30:03 PST
