From owner-chemistry@ccl.net Thu Nov 18 01:19:00 2010
From: "Victor Rosas Garcia rosas.victor%x%gmail.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: How to analyze a series of conformers
Message-Id: <-43178-101117165631-11316-gsdV3XHebrPatZRHza6LGw##server.ccl.net>
X-Original-From: Victor Rosas Garcia <rosas.victor*gmail.com>
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Date: Wed, 17 Nov 2010 15:56:24 -0600
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Sent to CCL by: Victor Rosas Garcia [rosas.victor^gmail.com]
Hello Sergio,

In order to spot duplicate or very similar structures, I use VMD to
load all the conformers, align them and calculate the RMS deviation
wrt one of the structures.  Depending on the quality of the energy
evaluation, sometimes conformers that seem somewhat different in
energy turn out to be basically the same conformer.

Don't know if this is the "best idea", as you requested.  Just my two cents.

Have a nice day

Victor

2010/11/17 Sergio Emanuel Galembeck segalemb-.-usp.br <owner-chemistry:_:ccl.net>:
>
> Sent to CCL by: Sergio Emanuel Galembeck [segalemb]_[usp.br]
> Hello,
>
>   I am doing a conformational analysis of an organic molecule.
> After the conformer generation and geometry optimization I
> obtained 38 low energy conformers. What is the best idea to analyze
> them, grouping conformers with similar conformations? Are there some
> free software that make this kind of analysis? Some years ago I did a
> work that used clustering techniques, but now I am curious if there are
> other techniques to do this kind of analysis.
>
>           Thanks,
>
>                 Sergio Emanuel Galembeck>    >       >
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>    >
>
>


From owner-chemistry@ccl.net Thu Nov 18 11:44:00 2010
From: "Kavi Sona kavisona7*_*gmail.com" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Douglas-Kroll-Hess calculation
Message-Id: <-43179-101118114100-17304-mj8JHQVcTn/Wa/0d9T2G6A,,server.ccl.net>
X-Original-From: "Kavi  Sona" <kavisona7/a\gmail.com>
Date: Thu, 18 Nov 2010 11:40:54 -0500


Sent to CCL by: "Kavi  Sona" [kavisona7-*-gmail.com]
Thank you very much for the valuable informations regarding Douglas-Kroll-Hess calculations.

by
Kavi


From owner-chemistry@ccl.net Thu Nov 18 13:46:00 2010
From: "Wolf D Ihlenfeldt wdi:-:xemistry.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: PubChem Assay Data available as KNIME native table files
Message-Id: <-43180-101118133321-2611-chjIumZ7QNyLJ1SK6RPr/g###server.ccl.net>
X-Original-From: "Wolf D Ihlenfeldt" <wdi###xemistry.com>
Date: Thu, 18 Nov 2010 13:33:18 -0500


Sent to CCL by: "Wolf D Ihlenfeldt" [wdi{}xemistry.com]
PubChem assay results, complete with structures, are now available for the KNIME data analysis system as native table files.

Free downloads from www.xemistry.com/pctables


Wolf-D. Ihlenfeldt, Xemistry GmbH (www.xemistry.com)