From owner-chemistry-!at!-ccl.net Sat Jul 6 15:20:00 2013 From: "N. Sukumar nagams,+,rpi.edu" To: CCL Subject: CCL: Tool to generate conformer database for ligand_like molecules Message-Id: <-48894-130706151008-1542-LSgHu5CSEGxjSRrQl5kqzA _ server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sat, 06 Jul 2013 15:10:15 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams[a]rpi.edu] Most of the popular cheminformatics and molecular modeling codes can do this. MOE from CCG (chemcomp.com) has both systematic conformation search and stochastic search options. You can set a maximum limit to the energy sampled and/or the number of conformations generated. N. Sukumar Professor of Chemistry Shiv Nadar University, India ---------------------------- "Pursue something so important that even if you fail, the world is better off with you having tried." -- Tim O'Reilly http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470769009.html ==============Original message text=============== On Fri, 05 Jul 2013 23:01:06 EDT "Bin Sun sunbinxod*gmail.com" wrote: Hello Everyone, I want to achieve all the possible conformations corresponding to the minimums on the potential surface of a ligand_like molecule. To this end, I firstly need to generate as many as possible conformers by rotating the rotatable bonds via some tools or software; Secondly, A sifting stage is performed in which the "bad" conformers having unfavorable energies are excluded. To ensure that there are no important conformations being omitted. the conformer database generated in the first step must be as completed as possible. Is there any tool or software that can generate completed conformer database for ligand_like molecules ? Thanks ! -Sun ===========End of original message text===========