Yes, these QM/MM boundaries in the backbone make most sense.
All the best,
Andy
On Feb 26, 2014, at 11:59 PM, Dmitry Nilov wrote:
> 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 Mar 06 2014 - 12:00:03 PST
