From owner-chemistry@ccl.net Sat Aug 19 00:55:01 2006 From: "Qing Zhang qzhang+*+scripps.edu" To: CCL Subject: CCL: Calculating whether a ligand is buried in a protein Message-Id: <-32410-060818221615-31117-rrywwblmWNfTIHntHQ+4RQ^-^server.ccl.net> X-Original-From: Qing Zhang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 18 Aug 2006 18:36:53 -0700 MIME-Version: 1.0 Sent to CCL by: Qing Zhang [qzhang===scripps.edu] Dear CCLers: Is there a standalone program that can calculate whether a ligand is buried in a protein, given the PDB coordinates of the ligand and the protein? Thanks, Qing -- ---------------------------------------------------------------- Qing Zhang, Ph.D. Molecular Graphics Laboratory Research Associate Department of Molecular Biology The Scripps Research Institute Tel: 858-784-2333 10550 North Torrey Pines Road Fax: 858-784-2860 Mail Drop: MB-5 Email: qzhang/./scripps.edu La Jolla, CA 92037 ---------------------------------------------------------------- From owner-chemistry@ccl.net Sat Aug 19 12:37:01 2006 From: "Jonas Baltrusaiti jonas-baltrusaitis---uiowa.edu" To: CCL Subject: CCL:G: neutralizing the charge in cluster Message-Id: <-32411-060819123630-17245-FSqD4SAz9N5P78lY9Rgryg a server.ccl.net> X-Original-From: "Jonas Baltrusaiti" Date: Sat, 19 Aug 2006 12:36:30 -0400 Sent to CCL by: "Jonas Baltrusaiti" [jonas-baltrusaitis-$-uiowa.edu] Dear ccl'ers, I want to optimize the structure ad calculate the valence band distribution on highly negatively charged cluster, e.g. FeO6 or Fe2O10. What approaches can I take to do the charge neutralization? Which software packages are best to use? Currently, I have access to Gaussian, GAMESS and ADF. Direct optmization with negative charge just tears the cluster apart in the process of minimization thanks Jonas