From chemistry-request@server.ccl.net Fri Sep 22 12:07:36 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA13982 for ; Fri, 22 Sep 2000 12:07:35 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Fri, 22 Sep 2000 18:10:01 +0200 Sender: zhang@ccl.net Message-ID: <39CB8291.73206A75@mail.biokemi.su.se> Date: Fri, 22 Sep 2000 18:02:25 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock: autotors Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear autodock experts, I got a problem to run "autotors" on some of my peptide models (the conformation of the peptide might not be realistic, but everyone was refined in molecular modeling program). I got the following error message: mol2flag = 0 hflag = 1 offset = 70 aflag = 1 bflag = 1 bnd format:94 records read in unable to attach all pieces of bond data Does anybody encountered a similar problem before? How to solve it? Thank you advance for any suggestions. Have a nice weekend? Sincerely, Zhang ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Fri Sep 22 13:55:13 2000 Received: from laplace.quimica.ufpr.br (laplace.quimica.ufpr.br [200.17.215.88]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA14393 for ; Fri, 22 Sep 2000 13:55:09 -0400 Received: from quimica.ufpr.br (localhost [127.0.0.1]) by laplace.quimica.ufpr.br (8.9.3/8.9.3) with ESMTP id OAA02508 for ; Fri, 22 Sep 2000 14:54:23 -0300 (EST) (envelope-from edulsa@quimica.ufpr.br) Sender: edulsa@laplace.quimica.ufpr.br Message-ID: <39CB9CCF.DFF831D2@quimica.ufpr.br> Date: Fri, 22 Sep 2000 14:54:23 -0300 From: Eduardo Lemos de Sa X-Mailer: Mozilla 4.74 [en] (X11; U; FreeBSD 4.1-STABLE i386) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Looking for DFT software Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCL's I am looking for (preferencially freeware) softwares that run (straightfowardly) optimization of geometry in complexes ions by DFT (including B3LYP). I'll summarize the responses Thanks in advance Eduardo -- Eduardo Lemos de Sá Prof. Dep. Química - UFPR Dep. Quimica - Centro Politecnico - Jardim das Américas P. Box 19081 81531-990 - Curitiba - PR - Brazil From chemistry-request@server.ccl.net Fri Sep 22 15:57:33 2000 Received: from castor.rice.edu (castor.rice.edu [128.42.81.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA14787 for ; Fri, 22 Sep 2000 15:57:32 -0400 Received: from localhost (knk@localhost) by castor.rice.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id OAA21742 for ; Fri, 22 Sep 2000 14:56:43 -0500 Date: Fri, 22 Sep 2000 14:56:42 -0500 (CDT) From: News user To: chemistry@ccl.net Subject: Summary: Geometry optimization of periodic systems In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A few days ago I asked the following question: > Dear collegues > > I am looking for references that describe geometry optimization methods > for periodic systems, and their applications. Specifically, I would like > to know about any algorithm that employs something more complicated than > the usual Cartesian coordinates for atomic positions and lattice vectors. > An example of such more elaborate method would be a variable-cell-shape > (VCS) algorithm which optimizes the dot products between the lattice > vectors instead of the Cartesian components of these vectors. > {I. Souza and J.L. Martins, Phys. Rev. B, 55, 8733 (1997).} > > Regards, > Konstantin Kudin Quite amazingly, the number of requests for a summary exceeded the number of informative replies. So here it is. The following algorithms currently seem to be available for optimization of periodic systems and are documented at least in some details in the literature: - a variable-cell-shape (VCS) algorithm, uses fractional coordinates for atoms within the cell and optimizes lattice vectors via their dot products. Originally developed for molecular dynamics, recently used for periodic system optimizations. The details about which Hessian is used seem to be unavailable. {I. Souza and J.L. Martins, Phys. Rev. B, 55, 8733 (1997).} Dr. Keith Refson provided some other references for earlier VCS dynamics algorithms. - the GULP computer program for periodic molecular mechanics, also uses fractional coordinates. The lattice vectors are optimized via the strain matrix with the 6 independent components. The GULP uses the exact Hessian computed once every few cycles. {http://www.ch.ic.ac.uk/gale/Research/gulp.html GULP - a computer program for the symmetry adapted simulation of solids, J.D. Gale, JCS Faraday Trans., 93, 629 (1997) } The info was provided by: Ricardo Grau-Crespo Centro de Investigaciones del Petroleo Unidad de Catalisis Washington 169 Esq. Churruca. Habana 12000 CUBA - a redundant internal coordinate algorithm for optimization of periodic systems. Both atomic positions and lattice vectors are optimized via a bunch of redundant internal coordinates. The method employs relatively expensive tranformations redundant internals <--> Cartesians, but permits high optimization efficiency with a simple diagonal guess for the Hessian. Therefore the method goes very well with expensive electronic structure calculations. {K.N. Kudin, G.E.Scuseria, H.B. Schlegel, J. Chem. Phys., submitted} Regards, Konstantin Kudin From chemistry-request@server.ccl.net Fri Sep 22 16:18:27 2000 Received: from server3.safepages.com (server3.safepages.com [216.127.146.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA14871 for ; Fri, 22 Sep 2000 16:18:27 -0400 Received: from quantumnt (5131-196-251.008.popsite.net [209.69.196.251]) by server3.safepages.com (Postfix) with SMTP id 7AEC322F66; Fri, 22 Sep 2000 16:18:12 -0400 (EDT) Message-ID: <000701c024d2$3b30cd40$0300a8c0@quantumnt> From: "Jim Kress" To: , "Reinaldo Pis Diez" References: <4.3.2.7.0.20000922003221.00a8d100@dalton.quimica.unlp.edu.ar> Subject: Re: CCL:Error message in G98 Date: Fri, 22 Sep 2000 16:18:11 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 You know, one would think that if Gaussian takes the time to put these error messages into their commercial code (for which people pay huge sums of money), they would at least publish a list of these error messages and their meaning. Even Microsoft does that. Why can't Gaussian? Jim ----- Original Message ----- From: "Reinaldo Pis Diez" To: Sent: Thursday, September 21, 2000 11:39 PM Subject: CCL:Error message in G98 > Dear ccl'ers, > > I'm running a frequency job with g98/linda under linux using the oniom > method. After some hours of calculation the program stops with the message > > Inv2: IOpt= 1 Iter= 1 AM= 3.91D-15 Conv= 1.00D-12. > Inverted reduced A of dimension 558 with in-core refinement. > D2ESCP-Res allocation failure: iend,mxcore= 617796 246369 > Error termination via Lnk1e in /usr/g98/linda-exe/l1002.exel. > > I increased the mem parameter by four wrt the first run (16mb vs 64mb) > but I got the same message in both cases. Maxdisk is set to 2gb. > What's the meaning of that "allocation failure" error? > Thanks in advance. > Regards, > > Reinaldo > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > >