From chemistry-request@server.ccl.net Sun Mar 23 04:12:29 2003 Received: from web15208.mail.bjs.yahoo.com ([61.135.128.138]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2N9CSr11403 for ; Sun, 23 Mar 2003 04:12:28 -0500 Message-ID: <20030323072541.32730.qmail@web15208.mail.bjs.yahoo.com> Received: from [202.119.32.49] by web15208.mail.bjs.yahoo.com via HTTP; Sun, 23 Mar 2003 15:25:41 CST Date: Sun, 23 Mar 2003 15:25:41 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: problems during GAMESS optimization To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I have encountered difficulties during my GAMESS geometry optimization. The molecule that I hope to optimize is acetylcholine, which has one positive charge. After about one and half hour, I get the following message in the GAMESS outfile. How should I do in the next? Thank you very much in advance! ***** Failure to locate stationary point, too many steps taken ***** Updated Hessian, geometry, and vectors will be punched for restart **** The geometry search is not converged! **** The next predicted set of coordinates follows. Their energy and gradient is unknown. You may prefer to restart with some other coordinates than these. You should restart "OPTIMIZE" runs with the coordinates whose energy is lowest. Restart "SADPOINT" runs with the coordinates whose RMS gradient is smallest. These are not always the last point computed! Sincerely yours, Jinsong Zhao zh_jinsong@yahoo.com.cn _________________________________________________________ Do You Yahoo!? 更多惊喜，同样精彩，NetVista A30 热卖 http://ad.cn.doubleclick.net/clk;5313999;7930402;p?http://www.ibm.com/cn/promotion/pc/netvista_a30/index.shtml From chemistry-request@server.ccl.net Sun Mar 23 13:19:03 2003 Received: from onsager.cop.uop.edu ([138.9.240.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2NIJ3r01649 for ; Sun, 23 Mar 2003 13:19:03 -0500 Received: from uop.edu (207-173-227-236.bras01.elk.ca.frontiernet.net [207.173.227.236]) by onsager.cop.uop.edu (8.11.6/8.9.3) with ESMTP id h2NID4J14743 for ; Sun, 23 Mar 2003 10:13:04 -0800 Date: Sun, 23 Mar 2003 10:19:00 -0800 Mime-Version: 1.0 (Apple Message framework v551) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: generating .crd from IC in CHARMM From: Charles McCallum To: chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: X-Mailer: Apple Mail (2.551) One of my students asked me a question about generation of cartesian coords from ICs in CHARMM (c27b4), and I couldn't answer it. When generating a DPPC in a three-residue (PALM, PCGL, PALM) way, we have been reading in an existing .crd file to specify the cartesian coords. The question was: "can't the ICs determine a set of cartesian coords?" We tried it, and what happens using the "ic seed" command is we get cartesians for only the residue that the seed atoms belong to. I've put an illustrative input file and the resulting .crd file here: http://onsager.cop.uop.edu/~mccallum/group-files/test.inp http://onsager.cop.uop.edu/~mccallum/group-files/ss01dppc.crd Can anyone explain to me why we're not getting a full set of coords? A second question regards the new version of CHARMM - c29. How useful will an upgrade be to us? WE run mostly aqueous amphiphilic and protein simulations, and must generate some of our own parameters. Cheers, Mike McCallum -- C. Michael McCallum http://chem.cop.uop.edu/cmmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. uop . edu (209) 946-2636 v / (209) 946-2607 fax From chemistry-request@server.ccl.net Sun Mar 23 18:02:22 2003 Received: from servm.fc.uaem.mx ([148.218.36.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2NN2Lr03918 for ; Sun, 23 Mar 2003 18:02:22 -0500 Received: from localhost (cmp@localhost) by servm.fc.uaem.mx (8.11.2/8.11.0) with ESMTP id h2NMuaj11047 for ; Sun, 23 Mar 2003 16:56:36 -0600 Date: Sun, 23 Mar 2003 16:56:36 -0600 (CST) From: Cesar Millan Pacheco To: Subject: Quasiharmonic Analysis on CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I want to run a Quasiharmonic Analysis on CHARMM of a protein (~2900 atoms) but I really don't understand how to implement the quasi module, or it's reduce form to treat these kind of problems. Some knows how to run it? Some have a script to run it? I really appreciate your help. -- Cesar Millan P. Facultad de Ciencias. Universidad Autonoma del Estado de Morelos