From owner-chemistry@ccl.net Fri Mar 21 01:13:00 2008 From: "Shuwen Yao lilichemistry(-)yahoo.com" To: CCL Subject: CCL:G: GaussView Cartesian coordinate setting Message-Id: <-36530-080321000232-13971-1eylyLt+3Bdx8NrluE8rkw_._server.ccl.net> X-Original-From: "Shuwen Yao" Date: Fri, 21 Mar 2008 00:02:29 -0400 Sent to CCL by: "Shuwen Yao" [lilichemistry_._yahoo.com] Hi,CCLers: I am using GaussView to darw species for G03 job. I am struck with the setting of Cartesian coordinate system. By default, the program has one, but that does not fit mine and I do not manage to change that one. So anyone could please show me the way to set the cartesian coordinate axes at will for any species in GaussView? Thanks a lot. Shuwen From owner-chemistry@ccl.net Fri Mar 21 07:00:01 2008 From: "Kalaiselvan Anbarasan kalaianbaccl(!)gmail.com" To: CCL Subject: CCL:G: Solvent calculations in Gaussian - doubts Message-Id: <-36531-080321065457-28710-3nLX7QiRR61WocKSm1n0gw(_)server.ccl.net> X-Original-From: "Kalaiselvan Anbarasan" Date: Fri, 21 Mar 2008 06:54:53 -0400 Sent to CCL by: "Kalaiselvan Anbarasan" [kalaianbaccl(-)gmail.com] Dear CCL members, When i tried to do a solvation of a gas phase optimized geometry using PCM model in Gaussian, I got the following error; ' Hint: increase the number of tesserae or change the molecule orientation Warning: electronic charge 965 neglected' Then i tried it again by increasing the TSNUM from the default value 60. But this time i got the following error ''Too many tesserae. Increase the MxTs' I got the same error, whatever TSNUM i have used. Kindly let me know your suggestions to overcome this problem in doing solvation. Thanking you in advance, Best regards Kalaiselvan From owner-chemistry@ccl.net Fri Mar 21 08:22:00 2008 From: "Gyorgy Pirok pirok]^[chemaxon.com" To: CCL Subject: CCL: Change Stereocenter specifically Message-Id: <-36532-080321073319-11727-OEvQ4LBIfQEyMQCxyQ2k8A_+_server.ccl.net> X-Original-From: "Gyorgy Pirok" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0058_01C88B49.33A0AA60" Date: Fri, 21 Mar 2008 11:46:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Gyorgy Pirok" [pirok#,#chemaxon.com] This is a multi-part message in MIME format. ------=_NextPart_000_0058_01C88B49.33A0AA60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, You might try the Reactor tool of ChemAxon = (http://www.chemaxon.com/jchem/doc/user/Reactor.html#stereo). You can = specify inversion on the corresponding atom at the reaction center and = batch run it on your molecules. You can run it from the GUI, but it is = even simpler to use the command line: react mymolecules.sdf -r inversion.rxn -o results.sdf -f sdf Best wishes, Gyorgy ------=_NextPart_000_0058_01C88B49.33A0AA60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 
You might try the Reactor tool of = ChemAxon (http:= //www.chemaxon.com/jchem/doc/user/Reactor.html#stereo).=20 You can specify inversion on the corresponding atom at the reaction = center and=20 batch run it on your molecules. You can run it from the GUI, but it is = even=20 simpler to use the command line:
 
react mymolecules.sdf -r inversion.rxn = -o=20 results.sdf -f sdf
 
Best wishes,
 
Gyorgy
------=_NextPart_000_0058_01C88B49.33A0AA60-- From owner-chemistry@ccl.net Fri Mar 21 16:23:00 2008 From: "Andrew Orry andy : molsoft.com" To: CCL Subject: CCL: MolSoft ICM Workshop - "Protein Structure and Drug Discovery" May 1-2 2008 Message-Id: <-36533-080321145153-13178-i/kfCa5cD/vluDe5p8mvbw%a%server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 21 Mar 2008 10:43:07 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy^^molsoft.com] MolSoft ICM Workshop: "Protein Structure and Drug Discovery" May 1-2 2008 La Jolla CA. Please accept this invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on May 1st to 2nd 2008 in La Jolla California USA. See www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. All workshops are presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft) and occasional guest speakers. The workshops will consist of lectures, demonstrations and "hands-on" computational experiments and cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, chemical clustering, searching, superposition ... - QSAR, machine learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D ligand editor - design new ligands interactively - Fully-flexible receptor-ligand docking - Multiple Receptor Docking - Automated model building into density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing movie making “The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools.” Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy(a)molsoft.com or call (858)625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology.