Thanks Jason.
On Fri, Apr 15, 2011 at 1:41 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> You can check the Amber manual under the QM/MM section. There are plenty
> of
> references included there. Google Scholar can also help.
>
> Good luck,
> Jason
>
> On Thu, Apr 14, 2011 at 11:23 PM, setyanto md <stwahyudi.md.gmail.com
> >wrote:
>
> > Dear jason
> > thank you very much for your respond
> > Do you have some literature on QMM calculation ? Would mind send to me
> the
> > QMMM literature, please.
> >
> > Thank you very much.
> > setyanto
> >
> >
> > On Fri, Apr 15, 2011 at 11:32 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > Hello,
> > >
> > > On Thu, Apr 14, 2011 at 9:25 PM, setyanto md <stwahyudi.md.gmail.com>
> > > wrote:
> > >
> > > > Dear amber user and developer
> > > >
> > > > I am doin qmmm simulation. I'd like to mask atom rather than residue.
> > > Here
> > > > is list of atoms from my pdb file:
> > > > :
> > > > ATOM 935 CG ASP 61 -4.452 12.837 -8.642 1.00 0.00
> > > > ATOM 936 OD1 ASP 61 -5.589 12.636 -8.154 1.00 0.00
> > > > ATOM 937 OD2 ASP 61 -3.962 13.964 -8.866 1.00 0.00
> > > >
> > > > I've been read in page 91 manual of Amber 10. we can use iqmatoms to
> > mask
> > > > our QM region.
> > > >
> > > > So I do like this :
> > > >
> > > > iqmatoms='.935,936,937',
> > > >
> > >
> > > No. This is an integer list. Just put "iqmatoms=935,936,937,"
> > >
> > >
> > > >
> > > > My question is :
> > > > 1. Is this correct or not ?
> > > > 2. How to calculate qmcharge according my QM definiiton? as I know
> that
> > > > charge of C is 0, O is -2, so total charge is -4, right or wrong ?
> > > >
> > >
> > > You have to determine how many electrons will be present total.
> > > Carboxylate
> > > groups typically only have a 1- charge. In case this is not just an
> > > example, performing QM/MM simulations *just* on a carboxylate group of
> a
> > > given residue doesn't seem like a realistic simulation to me. Consult
> > the
> > > literature (there is a lot of it) on QM/MM calculations to look into
> > common
> > > protocols.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > >
> > > > Thank you verymuch for your help.
> > > >
> > > > regards
> > > >
> > > > setyanto tri wahyudi
> > > > ITB-Biokimia
> > > > _______________________________________________
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 15 2011 - 02:00:02 PDT
