From: Thomas Patko <>
Date: Fri, 24 Aug 2007 10:43:35 -0700


Thanks for the reply. I was exactly wondering whether it
would make it into AMBER 10! If it yields significantly
better QM/MM as I suspect that it might, perhaps it is
worth a minor delay.



On Fri, 24 Aug 2007 09:36:26 -0700
  "Ross Walker" <> wrote:
> Dear Thomas,
>> Is there any interest (or more importantly time
>>allocated) to
>> implement
>> PM6 for the QM/MM module in AMBER
>> ( From
>> 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
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on
>request |
> Note: Electronic Mail is not secure, has no guarantee of
>delivery, may not
> be read every day, and should not be used for urgent or
>sensitive issues.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Aug 26 2007 - 06:07:44 PDT
Custom Search