From owner-chemistry@ccl.net Fri Jun 30 03:12:01 2006 From: "Anselm.Horn++chemie.uni-erlangen.de" To: CCL Subject: CCL: Reading EXTERNAL parameters in MOPAC7 Message-Id: <-32051-060629192252-8702-uj+/ipK59U59V/VQmeUE5Q * server.ccl.net> X-Original-From: Anselm.Horn**chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 30 Jun 2006 00:16:18 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn%a%chemie.uni-erlangen.de Hi, > We're getting problems reading parameters for new elements into Mopac7 > (Linux) with the EXTERNAL keyword. It doesn't work. For example, after > including the parameters for Se in a file and specifying this file with > the EXTERNAL keyword, a message is still produced > > DATA ARE NOT AVAILABLE FOR ELEMENT NO. 34 > SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH > NO PARAMETERS ARE AVAILABLE. CALCULATION STOPPED. > > I've found some old messages in CCL mentioning the same problem but > could not find an answer. Could anyone help? the problem probably arises, because you want to read in parameters for a *new* element; for one that is already known to Mopac all should be fine. I found a Mopac7 version on our system and scanned for your error message. It seems that in refer.f (called from the main program in mopac.f) a valid literature reference for the parameters of a certain element is used to decide where there really are parameters for that element; if not, your error message is printed. Unfortunately, the routine reading parameters from an external file (datin.f) does not read in or set the literature reference variable, and thus the literature reference test fails. My suggestion is to add a set of preliminary Se parameters directly in block.f, including of course a dummy literature reference (or just that one), and recompile. Thereafter, you should be able to read in and modify the parameters of the now existing element. Regards, Anselm From owner-chemistry@ccl.net Fri Jun 30 07:38:02 2006 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas__chem.elte.hu" To: CCL Subject: CCL: Re :CCL:G: SCF convergence Message-Id: <-32052-060629105757-6411-/5skQuMtzqQRhsvn7AvhcQ,,server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 29 Jun 2006 16:47:06 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas()chem.elte.hu] Hi Rajesh, Fortunately, if SCF converges to the right solution the optimization method does not alter the results (this also applies to geometry optimization) and QC just alters the optimization method. Using SCF=XQC is in general a good idea, since it switches to the more expensive QC only if regular SCF does not converge. If you are not sure that SCF converged to the right state you can use "Stable=Opt" to find the lowest energy state for sure. (Note: "Stable=Opt" and "Opt" - geometry optimization - cannot be used together.) Best wishes, Ödön -- Odon Farkas Research Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Fri Jun 30 08:13:00 2006 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas^-^chem.elte.hu" To: CCL Subject: CCL: G03: geom=connectivity Message-Id: <-32053-060630072310-2381-7RayXS251GqIssaWkmwxDw_._server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Fri, 30 Jun 2006 13:22:41 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas~!~chem.elte.hu] Hi Rajesh, Geom=Connectivity can affect the result of calculation only if molecular mechanics is used. Otherwise, it is useful, since it contains the topology of the molecule and there is no need to recalculate it for the purpose of visualization or data mining. Best wishes, Ödön On Thursday 29 June 2006 17:52, rajesh c rajesh_chinagandham_._rediffmail.com wrote: > Sent to CCL by: "rajesh c" [rajesh_chinagandham**rediffmail.com] > Dear users... > greetings. > what is the significanace of "geom=connectivity" .. OK it writes the > connectivity between atoms.. but how is this important in the > calculations..? and expecially if symmerty unrestrained calculation is > being done (i mean when the keyword "nosymm" is used) thanx in advance.. > > rajesh-- Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Fri Jun 30 09:06:00 2006 From: "Orlin Blajiev blajiev/a\vub.ac.be" To: CCL Subject: CCL:G: gaussian dump Message-Id: <-32054-060630090504-4859-wToFffOt4I6qjERhGllbAg*|*server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Jun 2006 15:05:11 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev%a%vub.ac.be] Hi, On the machine of the Computational Centre of our University the following problem with Gaussian arises. The write to the output is so rare that it is practically impossible to control the calculation unless it is finished (3 days!!) for example. I have a solution for programs which I can compile, but it does not work for Gaussian. I will appreciate some suggestions. Best regards, Orlin -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Fri Jun 30 12:43:01 2006 From: "Bhabani Mallik mbhabani~!~iitk.ac.in" To: CCL Subject: CCL: FFT in Xmgrace Message-Id: <-32055-060629034801-9375-om6U+3TMoL0jyI7yPy4jfg(_)server.ccl.net> X-Original-From: "Bhabani Mallik" Date: Thu, 29 Jun 2006 03:47:59 -0400 Sent to CCL by: "Bhabani Mallik" [mbhabani%a%iitk.ac.in] Can anyone help me how to perform fourier Transform with xmgrace? Thanks in advance, Bhabani From owner-chemistry@ccl.net Fri Jun 30 15:53:00 2006 From: "Maria Fernanda Zalazar mfzalazar!=!frre.utn.edu.ar" To: CCL Subject: CCL: AIMPAC compilation Message-Id: <-32056-060630133408-1569-TukIIG0iMICvjLbZlYO7iA]|[server.ccl.net> X-Original-From: "Maria Fernanda Zalazar" Date: Fri, 30 Jun 2006 13:34:05 -0400 Sent to CCL by: "Maria Fernanda Zalazar" [mfzalazar]![frre.utn.edu.ar] Hi all, I was interested in using the AIMPAC program from Bader's research group at McMaster University. I downloaded the source and I'd tried to install AIMPAC but failed. Has anybody had any experience with this compilation ? I am using SUSE 9.2 Any suggestion will be appreciated. Thanks all.