Hello,
it would be better to include the adaptive solvent QM/MM approximation in
that case. Please read the namelist &vsolv and &adqmmm in the qm/mm
section of the manual.
Greeting,
Hector.
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Héctor A. Baldoni
Profesor Adjunto
Departamento de Química
Área de Química General e Inorgánica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
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Received on Wed Oct 07 2015 - 04:30:03 PDT
