Thanks very much. I have added sever waters into the QM region and give them a small restraint. But it's possible to do steered MD with these restraint?
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> Today's Topics:
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> 1. How to do a QMMM calculation with a dynamic QM region (???)
> 2. Re: How to do a QMMM calculation with a dynamic QM region
> (Emilio Lence)
> 3. Re: How to do a QMMM calculation with a dynamic QM region
> (Hector A. Baldoni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 7 Oct 2015 17:18:00 +0800 (GMT+08:00)
> From: ??? <2011202030100.whu.edu.cn>
> Subject: [AMBER] How to do a QMMM calculation with a dynamic QM region
> To: amber.ambermd.org
> Message-ID:
> <4a0cd1d.28966.1504197d272.Coremail.2011202030100.whu.edu.cn>
> Content-Type: text/plain; charset=GBK
>
> 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 7 Oct 2015 11:55:20 +0200
> From: Emilio Lence <guitarro.de.meixente.gmail.com>
> Subject: Re: [AMBER] How to do a QMMM calculation with a dynamic QM
> region
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+yU+0tNkmivW78Wcx91W23ukx1kQxLur-dkx_oM=ur=EpLcOw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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 ??? <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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Emilio Lence Quintana
> Organic Chemistry Department-CIQUS
> University of Santiago de Compostela
> 15782 Santiago de Compostela, Spain
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 7 Oct 2015 08:05:53 -0300 (ARGSL-ST)
> From: "Hector A. Baldoni" <hbaldoni.unsl.edu.ar>
> Subject: Re: [AMBER] How to do a QMMM calculation with a dynamic QM
> region
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <1128.190.6.211.31.1444215953.squirrel.webmail.unsl.edu.ar>
> Content-Type: text/plain;charset=iso-8859-1
>
> 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 ????????? <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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Dr. Emilio Lence Quintana
> > Organic Chemistry Department-CIQUS
> > University of Santiago de Compostela
> > 15782 Santiago de Compostela, Spain
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --------------------------------------
> Dr. H?ctor A. Baldoni
> Profesor Adjunto
> Departamento de Qu?mica
> ?rea de Qu?mica General e Inorg?nica
> 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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> End of AMBER Digest, Vol 1365, Issue 1
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Received on Wed Oct 14 2015 - 02:30:03 PDT
