From owner-chemistry@ccl.net Tue Jul 26 09:56:47 2005 From: "CCL" To: CCL Subject: CCL: PCM with Bq atoms Message-Id: <-28928-050726094647-28616-ETc9kVj+VqHwexQEb/3djg:_:server.ccl.net> X-Original-From: lrrtldg:_:mta.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 MIME-Version: 1.0 Sent to CCL by: lrrtldg:_:mta.ca I am attempting to run PCM calculations with BSSE and water solvent within Gaussian 03. These MP2 calculations seem to have a problem with the Bq atoms and create an error "IA out of range in RList". Does anyone have any suggestions on how to get these calculations to run? Thank-you, Lesley Rutledge From owner-chemistry@ccl.net Tue Jul 26 11:04:14 2005 From: "CCL" server.ccl.net> To: CCL Subject: CCL: TD-DFT Message-Id: <-28929-050726095506-28959-ETc9kVj+VqHwexQEb/3djg<*>server.ccl.net> X-Original-From: Pablo Albores qi.fcen.uba.ar> Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Mime-Version: 1.0 Sent to CCL by: Pablo Albores qi.fcen.uba.ar> Hi, I was running a TD-DFT job with gaussian03 and the link died with the following message: "Unable to match L and R vectors in BiOrth " Anyone could tell me what is going on? Thank you very much for your time. Lic. Pablo Alborés INQUIMAE-FCEyN-UBA-ARGENTINA Ciudad Universitaria-Pab II-3 Piso Tel. 45763343 int. 127 Fax 45763341 From owner-chemistry@ccl.net Tue Jul 26 13:17:05 2005 From: "CCL" To: CCL Subject: CCL: atom typing in drug docking codes Message-Id: <-28930-050726130905-4019-ETc9kVj+VqHwexQEb/3djg^^^server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Mark Thompson I would like to hear from anyone with experience setting ligand atom types in drug docking programs. If a ligand has a carboxylate group, -COO(-) do programs like AutoDock, FRED, Glide, etc. treat it as -COO(-) or do they (or their GUI's) automatically turn it into a -COOH ? The results of a docking can vary dramatically depending on what is done with groups like this; do both oxygens of the -COO have the same atom type (I would say yes). How do these codes handle resonnance structures? For example the ring atoms of a purine: are they assigned atom types consistent with their aromatic status, or as non-aromatic sp2 from one of the resonannce structures? It makes most sense too me that there would be program defaults to make groups like -COO(-) the usual result, but also allow the user to change it to -COOH. I'm curious how these programs would handle docking large databases; presumably all ligands default to their "presumed" valence state in solution or in the active site. The reason this is bothering me right now is that I'm trying to validate some scoring functions and more often than not, the reason for disagreement is that the atom types are different. Cheers, Mark Thompson mark^^^arguslab.com http://www.arguslab.com From owner-chemistry@ccl.net Tue Jul 26 16:38:32 2005 From: "CCL" To: CCL Subject: CCL: atom typing in drug docking codes Message-Id: <-28931-050726161807-26880-ETc9kVj+VqHwexQEb/3djg:-:server.ccl.net> X-Original-From: "Pavel A. Petukhov" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" MIME-Version: 1.0 Sent to CCL by: "Pavel A. Petukhov" Mark, Sybyl and FlexX can handle COO- and other resonance structures as there are special atoms types for these cases. There is also a fully customizable Sybyl programming language (SPL) script (ionize.sh if I remember correctly) that can ionize a database of compounds and reassign the atoms types according to what expected under physiological pH. Autodock and DOCK can also handle the ionized compounds in a similar fashion. Pavel. ********* Pavel A. Petukhov Assistant Professor Department of Medicinal Chemistry and Pharmacognosy College of Pharmacy, (M/C 781) University of Illinois at Chicago 833 S. Wood St. Rm. 539 Chicago, IL 60612 phone: 312-996-4174 fax: 312-996-7107 Email: pap4:-:uic.edu Web: http://medchem.pharm.uic.edu/ ********* -----Original Message----- > From: owner-chemistry:-:ccl.net [mailto:owner-chemistry:-:ccl.net] Sent: Tuesday, July 26, 2005 12:27 PM To: Petukhov, Pavel A Subject: CCL: atom typing in drug docking codes Sent to CCL by: Mark Thompson I would like to hear from anyone with experience setting ligand atom types in drug docking programs. If a ligand has a carboxylate group, -COO(-) do programs like AutoDock, FRED, Glide, etc. treat it as -COO(-) or do they (or their GUI's) automatically turn it into a -COOH ? The results of a docking can vary dramatically depending on what is done with groups like this; do both oxygens of the -COO have the same atom type (I would say yes). How do these codes handle resonnance structures? For example the ring atoms of a purine: are they assigned atom types consistent with their aromatic status, or as non-aromatic sp2 from one of the resonannce structures? It makes most sense too me that there would be program defaults to make groups like -COO(-) the usual result, but also allow the user to change it to -COOH. I'm curious how these programs would handle docking large databases; presumably all ligands default to their "presumed" valence state in solution or in the active site. The reason this is bothering me right now is that I'm trying to validate some scoring functions and more often than not, the reason for disagreement is that the atom types are different. Cheers, Mark Thompson mark:-:arguslab.com http://www.arguslab.com