From owner-chemistry[ AT ]ccl.net Fri Feb 9 00:03:01 2007 From: "Wayne Steinmetz WES04747===pomona.edu" To: CCL Subject: CCL:G: ERROR in running gaussian Message-Id: <-33568-070208235958-8547-EUHSIZJ0NH8yFYOKuZpMkA|*|server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 8 Feb 2007 21:00:01 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747+*+pomona.edu] Although bonds are a human creation and are not required in a strictly ab initio quantum calculation, it helps to be heading in the right direction. Many programs including Gaussian require the Hessian which is often generated from molecular mechanics. I examined your pdb structure. It is very strange. The connectivity in the 5 aromatic rings is wrong. Two of the rings are not connected to the central antimony. It appears that you have a pentacoordinatd antimony(V) species. What is the source of the structure? Is it an X-ray structure? If so, the CHCl3 is a solvent of crystallization. Do you need it in the calculation? I am puzzled by the two OH's. Are they actually waters and two of the H's don't show up in the crystal structure because of crystal disorder. Many of the pdb files in the crystallographic databases are flawed. Once one knows the stoichiometry of the substance, once can patch up the structure and then move ahead. I would first start with a calculation at a lower level of theory, e.g. a semi-empirical calculation with a PM3 Hamiltonian. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz .. pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] Sent: Thursday, February 08, 2007 3:34 PM To: Wayne Steinmetz Subject: CCL:G: ERROR in running gaussian Sent to CCL by: "neeraj misra" [misraneeraj(0)gmail.com] I AM REPEATEDLY GETTING AN ERROR FOR THE FOLLOWING STRUCTURE WHOSE INPUT FILE I AM SENDING AS AN ATTACHMENT.THE GAUSSIAN PROCESSING SIMPLY CANNOT PROCEDD AFTER A FEW SECONDS.PLEASE HELP ME IN LOCATING THE ERROR. The Gaussian input file can be looked at: http://www.ccl.net/temp/TAN2OPTAMP1-inp.txt while the PDB file at: http://www.ccl.net/temp/TAN2-PDB.txt -- neeraj misra ab initio research lab department of physics lucknow university 226006 indiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software.