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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> > 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
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Received on Thu Apr 14 2011 - 23:30:03 PDT
