Subject: Conformational Analysis

From: Ramesh Gopalaswamy <[email-masked]>
Date: Fri, 24 Feb 1995 00:45:17 -0500 (EST)

I have been working with steroid conformational analysis in connection
with receptor modeling. I have generated several (typically 100) structures
(conformers) for each steroid using DGEOM program. Now I need to pick out
those conformers that are unique. (DGEOM generated structures might converge
to same minimum upon minimization). Any ideas on how to do that using
commercial modeling software or other shareware programs?
   Also, how to run minimizations (for 100 or so structures) as a background
job, instead of having to read in each structure on to the graphics 
interface? I have access to Quanta, Cerius2 and Sybyl. Thanks a lot.
Ramesh ([email-masked])

---

From: [email-masked] (Harry C. Johnson)
Date: Thu, 23 Feb 95 22:31:00 -0800

>>>>> "Ramesh" == Ramesh Gopalaswamy <[email-masked]> writes:

    Ramesh> I have been working with steroid conformational analysis
    Ramesh> in connection with receptor modeling. I have generated
    Ramesh> several (typically 100) structures (conformers) for each
    Ramesh> steroid using DGEOM program. Now I need to pick out those
    Ramesh> conformers that are unique. (DGEOM generated structures
    Ramesh> might converge to same minimum upon minimization). Any
    Ramesh> ideas on how to do that using commercial modeling software
    Ramesh> or other shareware programs?  Also, how to run
    Ramesh> minimizations (for 100 or so structures) as a background
    Ramesh> job, instead of having to read in each structure on to the
    Ramesh> graphics interface? I have access to Quanta, Cerius2 and
    Ramesh> Sybyl. Thanks a lot.  Ramesh ([email-masked])

I have recently finished enhancing Spartan's conformational analysis
methods.  I have implemented four new methods, including an interface
to DGEOM which automates the process of generating conformers, running
the appropriate optimizations, removing duplicates that may result
from the optimization, and finally calculating boltzman populations
based on the final conformers.  The other new methods that are
available, and are just as simple to use, are a simple systematic
search, a Monte Carlo search, and a Genetic Algorithm based search.

If you would like more information, send mail to [email-masked], or
directly to me.
-Harry

+-----------------------+--------------------------------------------+
|Harry C. Johnson       |  /--- ----\  /---/ ---\ ----- /---/ /|   / |
|Computational Chemist  |  \    /   / /   / /   /  /   /   / / |  /  |
|Wavefunction Inc.      |   \  /---/ /---/ /---/  /   /---/ /  | /   |
|E-mail: [email-masked]|---/ /     /   / /   \  /   /   / /   |/    |
+-----------------------+--------------------------------------------+