From owner-chemistry@ccl.net Fri Mar 4 07:46:00 2011 From: "Eliac Brown Eliacbrown*yahoo.com" To: CCL Subject: CCL: Autodock - Questions Message-Id: <-44050-110304074510-14820-UK+IxeeK4I6oLJ1mTW0pgA_._server.ccl.net> X-Original-From: "Eliac Brown" Date: Fri, 4 Mar 2011 07:45:08 -0500 Sent to CCL by: "Eliac Brown" [Eliacbrown*yahoo.com] Dear All I wan wondering if someone here could help me throughout autodock. I sent my email to autodock list, but I haven't got any reply. Here is my email, please any kind of help would be highly appreciated. ****** Dear ALL I couldn't understand some terms in Autodock, and I need a help please: * setminmax is a function to definethe minimum and maximum bond length between a couple of atoms, what is the aim of this function, as I believe autodock doesn't minimize the ligand structure? * How can I define explicity the setminmax in autodock tools? I need to make the bond between H-X constant, how? * What is the diffence between "Donor S Spherical Hydrogen" and "Donor 1 H- bond Hydrogen"? * How can I switch between Amber parameters and autodock parameters (pairewise)? * I am developing a new hydrogen atomtype, if I used XX atom type, the hydorgen bond will not be a directional bond, I couldn't replace the HD parameters with the new one where I am going to use both of them at the same time in the same molecule, what would you recommend? * I couldn't find reference for the volume and solvation parameter calculation, how you get these values for hydrogen (for example)? * partial charges: When I assigned partial charges of my protein using kollman method (all hydrogen explicit) and compared it to AMBER partial charges (using amber99SB force field), I found they are different, why? * Non-polar hydrogens are merged into the borne atom, in these case we call it united atom, how it is charge calculated? by adding the charge of the hydrogen atoms to the mother atom? if so, why the charge of the polar hydrogens are different between the two calculations? Please, any kind of help would be appreciated. Thanks in advance Eliac From owner-chemistry@ccl.net Fri Mar 4 08:21:00 2011 From: "psavita,+,crlindia.com" To: CCL Subject: CCL:G: Lone pair location Message-Id: <-44051-110303231827-26599-u2nYegaYdw6e5JTUWQsuKA{:}server.ccl.net> X-Original-From: psavita]_[crlindia.com content-transfer-encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 4 Mar 2011 09:53:21 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita:-:crlindia.com
Hello Joaquin,

The location and strength of lone pairs can b= e very well described by the topographical analysis
of molecular electros= tatic potential. Kindly refer to papers by S.R. Gadre and co-workers.
You= may calculate the electrostatic potential over a grid surrounding the molec= ule using Gaussian
and view the isosurfaces for qualitative insights.
=
Best Regards,

Savita Pundlik
Computational Materials Applied Research Group
Computatio= nal Research Laboratories Ltd.,
Taco House,= Damle Path, Off Law College Road
Pune - 411004, India.


-----owner-chemistry+psavita=3D=3Dcr= lindia.com-*-ccl.net wrote: -----

To: "Pundlik, Savita Sunil " <psavita-*-crlindi= a.com>
From: "Joaquin Calbo HimPhoenixCCL()gmail.com" <owner-che= mistry-*-ccl.net>
Sent by: owner-chemist= ry+psavita=3D=3Dcrlindia.com-*-ccl.net
Date: 03/03/2011 03:31PM
Subj= ect: CCL:G: Lone pair location


Sent to CCL by: "Joaquin  Calbo" [HimPhoenixCCL|-= |gmail.com]
Hello,

I would like to know about if exists any calcul= ations in Gaussian09 that help me to locate or visualize lone pair electrons= in order to assign the atom hybridation (O, S, N..). I tried with NBO analy= sis but I can't extract that information from it.

Thank you all.
=


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From owner-chemistry@ccl.net Fri Mar 4 09:44:01 2011 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre-.-univ-provence.fr" To: CCL Subject: CCL: Biophotochem workshop: last announcement. Message-Id: <-44052-110304083937-3481-NDaxASCS/q4W9rW4NM6U1Q#server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 4 Mar 2011 14:39:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre!=!univ-provence.fr] This is the last announcement of the workshop: "Modeling of biologically-inspired photoactive systems" that will be held in Marseille, France, from March 30 to April, 1st 2011. This workshop aims to bring together Europe-based recognized specialists, but also newcomers, young researchers and students that are involved in any theoretical development targeted or possibly applicable to the modeling of bio-photochemistry. Besides the presentation of well-established methods and their applications, the participants will be asked to present their up-to-date theoretical developments and to give their opinions about the future of such an intense research area, in terms of experimental-theoretical collaborations, needed new methodologies, ... The number of participants is limited to 50. Reduced fees are available to students and postdoctoral researchers (limited to 20 registrations). Deadline for registration and oral communication submission is march, 10th. A poster session will be open to all the participants. More information is available at http://sites.univ-provence.fr/lcp-ct/biophotochem/ See you in Marseille! Prof. Isabelle Demachy (Universite' Paris-Sud) and Dr. Nicolas Ferré (Universite' de Provence) Nicolas Ferre' Laboratoire Chimie Provence Universite' de Provence Phone : +33 413550532 From owner-chemistry@ccl.net Fri Mar 4 11:14:00 2011 From: "Shirley Peng speng]|[chemcomp.com" To: CCL Subject: CCL: MOE User Group Meeting - Speakers to Date Message-Id: <-44053-110304104534-23602-MQwEw5E67ds5F8ifYeK1aA ~~ server.ccl.net> X-Original-From: "Shirley Peng" Date: Fri, 4 Mar 2011 10:45:31 -0500 Sent to CCL by: "Shirley Peng" [speng^^^chemcomp.com] North American MOE UGM | June 20 -23, 2011 | Montreal, Canada Dear Friends & Colleagues, The MOE User Group Meeting is just around the corner. If you are interested in attending, I invite you to do so before March 18, 2011 and receive the reduced rate of $ 300 USD ($ 400 USD thereafter). Go to http://www.chemcomp.com/ugm-2011-register.htm to register online. More information about the meeting, including speakers, abstracts and training, can be found at http://www.chemcomp.com/ugm-2011.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scientific Presentations & Posters, June 22 23 // Speakers-to-Date: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Placing Trust in Docking Results: Is it even possible? Corbeil, Chris - Chemical Computing Group - QSAR with Phuzzy Pharmacophores Crippen, Gordon - University of Michigan - Talk title TBA Czerminski, Ryszard - AstraZeneca - Peptide conformational search by LowModeMD simulations Deng, Jinxia - Pfizer Animal Health - Reverse-docking of Cinchona Alkaloid Asymmetric Organocatalysis Deslongchamps, Ghislain - University of New Brunswick - Lessons Learned from Analyzing Structural Information from the PDB Duca, Jose - Novartis Institutes for BioMedical Research - Using Mutational Data To Drive Drug Design: Does It Really Work? Kondru, Rama - Hoffmann-La Roche - Visualizing Non-bonded Interactions Labute, Paul - Chemical Computing Group - Biomolecular Calculations Using NAMD and APBS with MOE Madura, Jeffry - Duquesne University - Some Thoughts on Analyzing Long Molecular Dynamics Trajectories Moreland, David IDSC - Computational Design of Potent HCV NS5A Compounds By Using MOE's Scaffold Replacement Technology Nicholas, John - InterMune - Let Gibbs Be Your Guide: Free Energy Simulations in Fragment-based Drug Design Reynolds, Charles Ansaris - BIpredict: MOE/web Server Enabled Delivery of in Silico Properties and Models Thompson, David C. - Boehringer Ingelheim - Applying Integral Equation Theory to Structure Based Design Truchon, Jean-Francois - Chemical Computing Group - Analysis of Fragment Libraries Using MOE Tsui, Vickie - Genentech - Rapid Assignment of Absolute Chirality using Vibrational Circular Dichroism Wesolowski, Steven - AstraZeneca ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Training & One-to-One Sessions, June 20 - 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Learn new tips and techniques from CCG support staff through courses covering key aspects of MOE. Dedicated one-on-one sessions with the CCG support staff will also be available for more in-depth discussions. To see the list of training offered at the UGM 2011 please visit our website at http://www.chemcomp.com/ugm-2011-training.htm ============================================================================ Thanks & have a great day! Shirley Shirley Peng Marketing Assistant Chemical Computing Group Tel: 514-393-1055146 | Fax: 514-874-9538 speng[A]chemcomp.com | www.chemcomp.com