Re: [AMBER] masking in the QMMM input

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 14 Apr 2011 23:41:43 -0700

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
> > > _______________________________________________
> > > 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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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 15 2011 - 00:00:02 PDT
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