Hello,
thank you for your suggestion. I don't think that the mask definition is the
source of the problem. I have successfully used this syntax in previous
simulations and I also tested the same input using PM3 -> everything was
working. Used mask matches with first 4 atoms in the structure:
(output for test with PM3):
.....................
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C -1.5731 1.7469 -0.9095
QMMM: 2 2 H -2.2504 1.8277 -1.7597
QMMM: 3 3 H -1.4412 2.6488 -0.3118
QMMM: 4 4 H -2.0047 1.0336 -0.2074
QMMM: 5 *H -0.5362 1.4912 -1.1275
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
....................
According to this output I believe that used syntax in mask is right.
Thanks, Zora
On Fri, Jul 23, 2010 at 3:39 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> A couple comments,
>
> On Fri, Jul 23, 2010 at 9:13 AM, Zora Strelcova <stre.chemi.muni.cz>
> wrote:
>
> > Dear Amber's Users.
> >
> > I have a problem with running QM/MM calculation in Amber 11. According to
> > the user manual the PM6 method should be available in this Amber version
> (
> > PM6 is supported for all elements which do not require d-orbitals).
> >
> >
> > In my tests the QM zone was defined as a mehtyle group and I would like
> to
> > try PM6.
> >
> > &qmmm
> >
> > qmcharge=0,
> > qm_theory=PM6,
> >
>
> Try using single-quotes to encompass the PM6. qm_theory='PM6'
>
>
> > qmmask='.1-4',
> >
>
> I think this mask is wrong. I've never actually seen numbers used after .,
> just atom names, but if it works with atom numbers in residues, then I
> think
> it might match the first 4 atoms of each residue... In any case, review
> the
> ambmask syntax and make sure this is what you're trying to do.
>
> Good luck!
> Jason
>
> writepdb=1,
> >
> > qmshake=0,
> > qm_ewald=1,
> > qm_pme=1
> > /
> >
> > Such calculation ends with error message:
> > "SANDER BOMB in subroutine read_qmmm_namelist
> > PM6 not currently supported in sander.
> > (qm_theory = 'PM6')"
> >
> > I would appreciate if you can explain me this issue. Is PM6 really
> > implemented and if so where can be the source of my problem?
> >
> > Thanks in advance, Zora
> >
> >
> > --
> > ==========================================
> > Zora Strelcova
> > ==========================================
> > National Centre for Biomolecular Research (NCBR)
> > Faculty of Science, Masaryk University
> > Kotlarska 2, 611 37 Brno, Czech Republic
> > =========================================
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
==========================================
Zora Strelcova
==========================================
National Centre for Biomolecular Research (NCBR)
Faculty of Science, Masaryk University
Kotlarska 2, 611 37 Brno, Czech Republic
=========================================
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Received on Fri Jul 23 2010 - 07:00:05 PDT
