Subject: Re: Conformational search, Alchemy 2000 vs MM3

From: David Gallagher <[email-masked]>
Date: Fri, 22 Nov 2002 15:26:06 -0800

Hi Adel,

CONFLEX (H. Goto & E. Osawa, J. Chem. Soc. Perkin Trans 2, 187-198, 1993) 
in BioMedCAChe automatically generates all ring conformations, then energy 
minimizes them with MM3 or MM2, discards redundant structures and saves a 
list of all minima (within a specified range) including the global minimum. 
The process is fully automated and can be performed on a whole batch of 
molecules with just a single mouse click. The calculations can run on 
Windows, Macintosh or a UNIX server. An evaluation version of BioMedCAChe 
is available from http://www.cachesoftware.com/biomedcache/index.shtml

David Gallagher, Fujitsu

At 03:54 PM 11/21/2002 +0300, Adel El-Azhary wrote:
>Deae CCL users:
>
>I am doing conformational search using the Alchemy 2000 program. It looks 
>that my molecule has a large ring of 18 atoms and the number of possible 
>conformations is quite large and taking a quite lot of effort. This is 
>because I create say 200 conformations and then do MM3 geometry 
>optimization on each manually and then examine each output. I have to 
>repeat this step for about a 100 time. I was thinking that the MM3(2000) 
>program running on unix might be more firiendly. Does anyone has a 
>suggestion or a similar experience.
>
>Best regards,
>
>Adel El-Azhary