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
> =========================================
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jul 23 2010 - 07:00:03 PDT
