You can also set 'writepdb=1' in the qmmm namelist and you will get a pdb
written out with the quantum atoms (and link atoms) in it for you to check.
All the best
Ross
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Wednesday, August 17, 2011 10:39 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to specify a quantum region of a system
>
> Use the "ambmask" program if you want to see what atoms are selected
> based
> on a given mask.
>
> HTH,
> Jason
>
> On Wed, Aug 17, 2011 at 1:19 PM, Aimin <aimin.guo.csun.edu> wrote:
>
> > Dear Amber users,
> >
> > I can use the command qmmask=': residue number1, residue number2,
> ...' to
> > specify the quantum region of a system, where the residue number is
> obtained
> > from the term "FLAG RESIDUE_LABEL" of the prmtop file. Is it right?
> >
> > For example, I have built a system which consists of 10 DNA base-
> pairs,
> > counterions, and solvent. If the 10 DNA base-pairs are treated
> quantum
> > mechanically, I should use the command qmmask=':1-20'. Is it right?
> >
> > Thanks.
> >
> > Aimin
> >
> > _______________________________________________
> > 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 Wed Aug 17 2011 - 14:00:04 PDT
