Hi.
If the waters that are near the drug are being exchange with the bulk
solvent, when you put them in the QM region you should put a weak
restriction in order to prevent that the QM waters move further from the
rest of the QM region, because in that case you will have problems with the
calculation. I will use a restriction with a small constraint to prevent
the waters to move further than 5 A, for example, but no restriction
applied ny they are closer. This way you give some freedom of movement to
the water molecules, but prevent that the QM region become too big.
Hope it is useful
Emilio Lence
2015-10-07 11:18 GMT+02:00 崔克新 <2011202030100.whu.edu.cn>:
> Hello!
>
> I'm doing a QMMM calculation for a drug molecule and protein and i want to
> know the effect of water for this process. So i want to set the QM region
> as the drug molecule, the binding site, and the waters whthin 4 anstroms
> arroud the drug. It's hard to put waters into QM region because waters are
> moving from this region and into this region.
>
> So how to do QMMM calculation in this case?
>
> Thanks for your any suggestion!
>
> Best regards
>
> Kexin CUI
> 05/10/2015
>
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--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Wed Oct 07 2015 - 03:00:02 PDT
