Dear Jason,
Thanks very much for your kind help! I use "qmmask" and it works well!
2013/9/27 Jason Swails <jason.swails.gmail.com>
> On Thu, Sep 26, 2013 at 11:05 PM, Cuiyl <cuiyinglukitty.gmail.com> wrote:
>
> > I checked the min1.out file, following are the error massage:
> > QM ATOM VALIDATION: nquant has a value of 0
> > which is bigger than natom of 73626. Need 0 < nquant <= natom.
> > SANDER BOMB in subroutine validate_qm_atoms
> > nquant illegal
> > Need 0 < nquant <= natom
> > I rewrite the min.in:
> > &qmmm
> >
> >
> >
> iqmatoms='.6068-6075,6098-6105,8252-8261,11263-11268,13185-13187,13190-13191,13195-13197,13201-13202,13204-13225,13237-13242',
> > qmcharge=-1,
> > qm_theory=PM3,
> > qmshake=1,
> > qm_ewald=1, qm_pme=1
> > /
> > but the error also occurred. How to set the value of iqmatoms?
> >
> > [snip]
> >
> > >
> > >
> >
> iqmatoms='.6068-6075,6098-6105,8252-8261,11263-11268,13185-13187,13190-13191,13195-13197,13201-13202,13204-13225,13237-13242',
> > > qmcharge=-1,
> > > qmtheory=1,
> > > qmshake=1,
> > > qm_ewald=1, qm_pme=1
> > > /
> > >
> >
>
> I suggest checking the QM/MM part of the Amber12 manual and looking at the
> variable descriptions. iqmatoms, for instance, expects a
> "comma-separated integer list containing the atom numbers (from the
> prmtop file)
> of the atoms to be treated quantum mechanically." It will not understand
> masks or strings. So it should not be surrounded by quotes, there should
> be no leading "." in front of the list, and most importantly there should
> be no atom ranges (I think the namelist parser will evaluate 11263-11268
> and assume you want to treat atom -5 quantum mechanically).
>
> You can use a mask instead of a list of atom numbers by using the "qmmask"
> variable instead. And as always, if you are having problems in parallel
> try running with serial first to see if that works. (Parallel scaling in
> QM/MM simulations will be quite limited, however, due to the poor
> scalability of semi-empirical methods.)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
*Ying-Lu Cui*
State Key Laboratory of Theoretical and Computational Chemistry,
Institute of Theoretical Chemistry,
Jilin University,
Changchun 130023,
P. R. China
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Received on Fri Sep 27 2013 - 05:00:03 PDT
