Dear Dmitriy,
You cannot run QM/MM without a prmtop file for the whole complex, including
the QM atoms.
Although partial charges and bonded parameters will not be used within the
QM region, van der Waals parameters are - in the QM/MM hamiltonian, van der
Waals interactions between QM and MM atoms are calculated using the MM van
der Waals interaction term. So you could choose existing atom types that
are chemically similar to those in your ligand (so that the van der Waals
parameters are sensible), and make up some 'bogus' charges & bonded
parameters for atoms that will be fully in the QM region.
(Note that metals may require sophisticated QM levels to get right - you
should at least be very careful with this).
Hope this helps,
Marc
On 2 September 2014 08:29, Spelnikov Dmitriy <pilule.yandex.ru> wrote:
>
> Dear Collegues,
>
> Thank you for amber package. It is nice to use it. But I have some
> question.
> I think, that amber treat QM region in QMMM without using MD atom
> types. I
> want to treat metal ions and ligands without using prmtop and topology
> files
> for them. How to do that? Is it correct to use prmtop and topology
> files for
> protein only for QMMM, when I calculate complex i.e.
> protein+metal+ligand?
> QM use for GAF-prmtop file. For meny atoms (metals and in ligands) AMBER
> field have no parameters. So I want to calculate such atoms directly
> using
> QMMM. But sender needs prmtop file for the hole molecular complex:) How
> to
> calculate QMMM directly without prmtop file for QM region?
>
> Thank you in advance!
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 02 2014 - 02:00:02 PDT
