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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Received on Fri Sep 27 2013 - 04:30:02 PDT
