I would say you are correct about the mask. What about putting quotes
around the PM6? The version of the source code I see options for PM6, so I
think it should work...
Good luck!
Jason
On Fri, Jul 23, 2010 at 9:54 AM, Zora Strelcova <stre.chemi.muni.cz> wrote:
> 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
> =========================================
> _______________________________________________
> 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
Received on Fri Jul 23 2010 - 07:30:03 PDT
