From owner-chemistry@ccl.net Mon Feb 24 03:08:00 2014
From: "Michel Petitjean petitjean.chiral[#]gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Molecular shape index values
Message-Id: <-49797-140224030655-5878-itSRKv7pqo9GdqlhdUFvjQ+*+server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral%a%gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 24 Feb 2014 09:06:49 +0100
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Sent to CCL by: Michel Petitjean [petitjean.chiral||gmail.com]
What do you mean by the "molecular shape for the benzene derivatives" ?
There are many shape descriptors, and the ones to retain depend on why
you need them
(e.g. the shape may be a sphere, a cylinder, a convex polyhedron, etc.)
RADI computes several ones: look at the bottom of
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

Best regards,

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral()gmail.com (preferred),
        michel.petitjean()univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html


2014-02-23 19:44 GMT+01:00 bellifa khadidja kbellifa-.-yahoo.com
<owner-chemistry()ccl.net>:
>
> Sent to CCL by: "bellifa  khadidja" [kbellifa[*]yahoo.com]
> What is the best method (experimental, theoritical) to obtain the molecular shape for the benzene derivatives?


From owner-chemistry@ccl.net Mon Feb 24 09:08:00 2014
From: "kathryn emily kellett k.kellett _ herts.ac.uk" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Energy conformers for ligands in bund protein structures
Message-Id: <-49798-140224063950-32622-0imtK0aZiFMDCmXYUEed4g~~server.ccl.net>
X-Original-From: "kathryn emily kellett" <k.kellett%x%herts.ac.uk>
Date: Mon, 24 Feb 2014 06:39:44 -0500


Sent to CCL by: "kathryn emily kellett" [k.kellett]=[herts.ac.uk]
I am trying to find a way of comparing the energy of my ligand in my protein from the PDB with a minimum energy conformation in vacuo. Does anyone know any way of doing this using either Maestro (for which I have a licence) or using freely accessible software.

I want to make sure I am comparing like with like, ie both in vacuo rather then orientation in crysal structure with solvation energies taken into account. 

thanks,

Katy k.kellett~~herts.ac.uk


From owner-chemistry@ccl.net Mon Feb 24 09:43:00 2014
From: "Juliette Pradon pradon+*+ccdc.cam.ac.uk" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: Docking and covalent bonds
Message-Id: <-49799-140224085218-19444-UNx87URgxW7cVfCZQnK2iA]-[server.ccl.net>
X-Original-From: "Juliette  Pradon" <pradon^_^ccdc.cam.ac.uk>
Date: Mon, 24 Feb 2014 08:52:11 -0500


Sent to CCL by: "Juliette  Pradon" [pradon###ccdc.cam.ac.uk]
Dear Jim, 

You are right in that GOLD has a covalent docking capacity. To model binding/unbinding (i.e. a chemical reaction), however, requires electrons to be able to move, and for this process a quantum mechanics model is required. This is not possible with GOLD or with any other software from the Cambridge Crystallographic Data Centre. 

Best regards,
Juliette Pradon.

>Sent to CCL by: "Jim Kress" [jimkress35!^!gmail.com]
>While I am aware there is a covalent bonding "capability" in AutoDock
>and
>GOLD, is there any information about the quality of its description of the
>covalent bonding process (making and breaking bonds)?
>Any references would be appreciated.
>Thanks.
>Jim