From: Ross Walker <>
Date: Fri, 24 Aug 2007 09:36:26 -0700

Dear Thomas,

> Is there any interest (or more importantly time allocated) to
> implement
> PM6 for the QM/MM module in AMBER
> ( From my
> work with some
> model heme model systems, it seems to produce better geometries than
> AM1, RM1 and PM3.

I plan to do this however at present the PM6 Hamiltonian is not public
domain and so we cannot legally add it and I don't have the parameters to do
it. However, I was in discussion with James Stewart at ACS and the PM6
implementation and parameters are going to be published in the near future
at which point it will be considered public domain and can be implemented
into other packages. James Stewart wants to wait until the proof stage
before sending me a copy due to the problems that typos etc in parameters
sets could pose. Hence as soon as I get this and a comprehensive set of
things I can test against I will work to add PM6 support. Whether this can
make it into Amber 10 or not before release I don't know at the moment and
will largely depend on factors outside my control.

Note in the meantime PM3/PDDG does a pretty good job from our tests to date.
How much better PM6 will be over this I'm not sure.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Aug 26 2007 - 06:07:43 PDT
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