From owner-chemistry@ccl.net Fri Mar  6 12:01:00 2009
From: "David Gallagher gallagher.da]_[gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL:G: QM/MM question
Message-Id: <-38777-090306102612-5305-3bMyOfKH7ok6n7Bjyh5K8g^_^server.ccl.net>
X-Original-From: David Gallagher <gallagher.da_._gmail.com>
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Date: Fri, 06 Mar 2009 07:25:56 -0800
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Sent to CCL by: David Gallagher [gallagher.da/a\gmail.com]
Hi Maurizzio,

Another option to consider for "geometry optimizations, transition 
states, etc. in protein systems" would be the new MOPAC2009 quantum 
chemistry program. Its linear scaling algorithm can handle geometry 
optimizations of up to 15,000 atoms.

The new PM6 method in MOPAC2009 was parameterized primarily for 
biological systems, and there is a bibliography at 
http://www.cacheresearch.com/mopac.html#mopac-support .

MOPAC2009 is free for academic non-profit use.

Good luck,
David Gallagher
CACheResearch.com


At 10:08 PM 3/5/2009, Maurizzio m.argonni[]gmail.com wrote:
>Dear CCL'ers:
>
>I would like to perform some QM/MM calculations but I don't seem to 
>be able to find adequate software for it that is free for academic 
>use. Are the choices really so limited? So far, I am aware of GAMESS 
>interfaced to a very dated version of Tinker and then QMMM software 
>from Dr. Truhlar's lab that is able to use also GAMESS and Tinker 
>albeit in a limited way because of limitations in GAMESS.
>
>I have no money to pay for Gaussian or Schrodinger's Qsite and I 
>sort of refuse to pay 500 UK Pounds for Chemshell on the basis that 
>I am not British (not to mention that most of the software they use 
>as a base for theirs is free and/or developed elsewhere).
>
>Anyway, I would appreciate any insights into what choices I have 
>for  QM/MM software that would allow me to do calculations like 
>geometry optimizations, transition states, etc. in protein systems. 
>Thanks for the help!
>
>Maurizzio
>
>