From owner-chemistry@ccl.net Mon Aug 7 06:34:00 2006 From: "Carsten Detering detering]=[biosolveit.de" To: CCL Subject: CCL: 4th FlexX Docking Workshop - Agenda set-up Message-Id: <-32349-060807063007-32084-s8GnYuPjs9hoPW+DDRCnkg[*]server.ccl.net> X-Original-From: "Carsten Detering" Date: Mon, 7 Aug 2006 06:30:06 -0400 Sent to CCL by: "Carsten Detering" [detering..biosolveit.de] Dear CCLers, it is merely one month till the 4th FlexX Training Workshop in Santa Clara, CA, USA. This is just a quick reminder that we can only guarantee for your spot in this premier event if you have registered via our web site (www.biosolveit.de/workshops/2006/registration.html) and if the registration fee has been paid in full. Workshop Agenda: Wednesday, September 6: Welcome Reception, TBA Thursday, September 7: 8:30 - 9:15 Getting Started 9:15 - 10:00 The Workflow Picture Coffee Break 10:15 - 10:45 Overview over the Environment 10:45 - 12:00 Ligand Preparation Lunch 13:00 - 14:15 Receptor Preparation Coffee Break 14:30 - 16:00 Docking Procedure Coffee Break 16:15 - 17:00 Extension Modules: FlexX^C, FlexX-Ensemble Coffee Break 17:15 - 18:30 Extension Modules: FlexX-Pharm Friday, September 8: 8:30 - 10:00 Configuration / Transforms Coffee Break 10:15 - 11:15 Scripting / Parallelization Coffee Break 11:30 - 12:30 Parameter Lunch 13:30 - 15:00 Scoring Coffee Break 15:15 - 15:45 TBA 15:45 - 16:15 TBA The agenda can also be found on the Workshop web site, www.biosolveit.de/workshops/2006 Please note that the agenda may be subject to change. Register now to become a FlexX master! Your FlexX developers, -BioSolveIT From owner-chemistry@ccl.net Mon Aug 7 10:30:00 2006 From: "=?ISO-8859-1?Q?=C5smund_Rinnan?= asmundrinnan(~)gmail.com" To: CCL Subject: CCL:G: Problems with running Gaussian 03 Message-Id: <-32350-060807054259-29060-mPaOqJp7fVO88Aub2xF8Lw],[server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 7 Aug 2006 11:02:12 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" [asmundrinnan : gmail.com] Hi, I've just installed Gaussian03 on a Linux computer using Slackware 10.2 system, with Linux version 2.4.26. The computer has 512Mb SDRAM in memory and has a CPU of 2.8GHz. However, upon starting a job it stops after executing l1.exe, it never starts l101.exe. Does anybody have a solution for this problem? Gaussian03 was not installed as root, but as far as I understand that should not be a problem. Best regards, Åsmund Rinnan Quality & Technology Food Science Royal Veterinary and Agricultural University Denmark From owner-chemistry@ccl.net Mon Aug 7 11:05:00 2006 From: "Nicolas Staelens nicolas.staelens###fundp.ac.be" To: CCL Subject: CCL: TINKER pdbxyz routine Message-Id: <-32351-060807030930-5366-AA+PzJeLLvMgYVhXJU78SQ-#-server.ccl.net> X-Original-From: Nicolas Staelens Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 07 Aug 2006 08:30:17 +0200 Mime-Version: 1.0 Sent to CCL by: Nicolas Staelens [nicolas.staelens__fundp.ac.be] At 05:13 7/08/2006, you wrote: >Sent to CCL by: "Gregory Tawa" [gtawa#,#hotmail.com] >To all >Recently I have been looking at the TINKER modeling package (J. Ponder >group). I have been using it to calculate protein-protein interaction >energies just fine. > >Lately however I have tried to calculate ligand-protein interaction energies. >The first step is to use the pdbxyz routine to convert a pdb file >(containing a ligand-protein complex) into a TINKER xyz file. >The problem is that when using pdbxyz to do the conversion, the ligand >drops out. In fact all HETATM fields drop out. In the end I get an xyz >file with just the protein. > >Am I missing something? Or do I have to develop some kind of work around >to fix this problem. > >Does anyone have a solution to this problem? > >Thanx > >GregHello, You can use the Open Babel software to convert molecular file formats : http://openbabel.sourceforge.net/wiki/Babel http://sourceforge.net/projects/openbabel/ From owner-chemistry@ccl.net Mon Aug 7 12:32:00 2006 From: "Chris Van Dyke vandyke]^[tripos.com" To: CCL Subject: CCL: Tripos Training Workshops 2006 Message-Id: <-32352-060807122404-19520-pZU31dnbQER9LD3vfBYgSQ^^server.ccl.net> X-Original-From: "Chris Van Dyke" Date: Mon, 7 Aug 2006 12:24:03 -0400 Sent to CCL by: "Chris Van Dyke" [vandyke()tripos.com] Tripos is pleased to remind you of the Training Workshop schedule for the remainder of 2006. These courses are designed to help you make the most efficient and productive use of your Tripos software. LIGAND-BASED MODELING FOR NEW MODELERS Munich, Germany. September 5-6, 2006 St. Louis, MO, USA. September 12-13, 2006 RECEPTOR-LIGAND MODELING FOR NEW MODELERS Milton Keynes, UK. October 17-18, 2006 St. Louis, MO, USA. October 24-25, 2006 Edison, NJ, USA. December 5-6, 2006 PROTEIN MODELING FOR NEW MODELERS St. Louis, MO, USA. November 7-8, 2006 3D-DATABASE SEARCHING Milton Keynes, UK. October 20, 2006 St. Louis, MO, USA. November 10, 2006 Paris, France. November 15, 2006 COMBINATORIAL LIBRARY DESIGN Munich, Germany. December 7-8, 2006 DESIGNING ACTIVE LIGANDS WITH QSAR/COMFA Munich, Germany. September 7-8, 2006 St. Louis, MO, USA. September 14-15, 2006 Paris, France. November 16-17, 2006 PHARMACOPHORE MODEL ANALYSIS St. Louis, MO, USA. November 9, 2006 VIRTUAL SCREENING St. Louis, MO, USA. August 22, 2006 Milton Keynes, UK. October 19, 2006 St. Louis, MO, USA. October 26, 2006 Paris, France. November 14, 2006. Munich, Germany. December 5, 2006 Edison, NJ, USA. December 7, 2006 For course descriptions, pricing information and registration, please visit http://www.tripos.com/training. You may send questions concerning these Training Workshops to training^tripos.com. ============================= Chris Van Dyke, Ph.D. Director, Scientific Training Tripos, Inc. ============================= From owner-chemistry@ccl.net Mon Aug 7 15:30:00 2006 From: "Deepangi Pandit Deepangi.Pandit{}gmail.com" To: CCL Subject: CCL: Bond Parameters - Trimethylsilyl group Message-Id: <-32353-060807152914-16429-vb35gPsDzJ+Zl+OEsVKPVg:_:server.ccl.net> X-Original-From: "Deepangi Pandit" Date: Mon, 7 Aug 2006 15:29:14 -0400 Sent to CCL by: "Deepangi Pandit" [Deepangi.Pandit : gmail.com] Hello All: I want to do molecular modeling for the trimethylsilyl group [C-Si-C]. C I am using SYBYL. I was wondering if anybody has bond parameters for this group. Thank you, Deepangi Pandit Deepangi.Pandit:gmail.com