From chemistry-request@server.ccl.net Mon Jul 12 04:59:49 1999 Received: from cmcind.far.ruu.nl (cmcind.pharm.uu.nl [131.211.56.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA14012 for ; Mon, 12 Jul 1999 04:59:48 -0400 Received: from pharm.uu.nl (fischer.far.ruu.nl [131.211.56.46]) by cmcind.far.ruu.nl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id KAA16108; Mon, 12 Jul 1999 10:51:43 +0200 (MDT) Sender: moret@pharm.uu.nl Message-ID: <3789AC9E.530E08AA@pharm.uu.nl> Date: Mon, 12 Jul 1999 10:51:42 +0200 From: "Ed E. Moret" Reply-To: E.E.Moret@pharm.uu.nl Organization: Utrecht University X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Mopac93/COSMO DOES like my Zwitter ion Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL The definitive answer to my question regarding Mopac93 and Zwitter ions is: Zwitter ions are unstable in vacuum. Use Cosmo (keyword eps=78.4) to simulate solvation or add solvent/counterions. After recompiling in order to enable Cosmo, the new screening worked wonders. Even some experimental evidence is given in J. Am. Chem. Soc. 1998 120 5098 Thank you very much Thomas Wyttenbach and many thanks as well to John M. McKelvey Hajime Takashima Andrey Bliznyuk Antonio Morreale Ansgar Schuffenhauer William A. Wylie Jose I. Garcia With best regards Ed Moret -- | Ed E. Moret (@more@) Department of Medicinal Chemistry | Faculty of Pharmacy Utrecht University The Netherlands | Tel.: +31 30 2536979(2536958) Fax: +31 30 2536655 | E-mail: E.E.Moret@pharm.uu.nl WWW: http://wwwcmc.pharm.uu.nl/moret/ From chemistry-request@server.ccl.net Mon Jul 12 05:11:32 1999 Received: from CHEMNA.DICHI.UNINA.IT (chemna.dichi.unina.it [192.135.165.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA14194 for ; Mon, 12 Jul 1999 05:11:31 -0400 From: MONACO@CHEMNA.DICHI.UNINA.IT Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V5.2-29 #30460) id <01JDH3AMMY3Q0000K8@CHEMNA.DICHI.UNINA.IT> for CHEMISTRY@www.ccl.net; Mon, 12 Jul 1999 11:04:56 CET Date: Mon, 12 Jul 1999 11:04:54 +0100 (CET) Subject: surface energy To: CHEMISTRY@server.ccl.net Message-id: <01JDH3AMPCX40000K8@CHEMNA.DICHI.UNINA.IT> X-VMS-To: CHEMISTRY@www.ccl.net MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers, I am interested in the structure and stability of surfaces of ionic crystals. While it is reltively easy to find references of surface studies on metals, it is not so for ionic crystals. In particular I was unable to find references either collecting a list of stable surfaces of ionic compounds, or describing methods to evaluate the surface energy of such compunds. I wounder if any of you can help me. I will summarize, if the topic is of interest. Thanks a lot Guglielmo Monaco PhD student Via Mezzocannone, 4 Dipartimento di Chimica Universita' di Napoli - ITALY e-mail: monaco@chemna.dichi.unina.it From chemistry-request@server.ccl.net Mon Jul 12 06:31:52 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA14910 for ; Mon, 12 Jul 1999 06:31:52 -0400 Received: from uia.ac.be by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id MAA03515; Mon, 12 Jul 1999 12:25:33 +0200 (MET DST) Sender: roussea@uia.ua.ac.be Message-ID: <3789BF3F.18D4BDDF@uia.ac.be> Date: Mon, 12 Jul 1999 12:11:11 +0200 From: Bart Rousseau Organization: University of Antwerp (UIA) X-Mailer: Mozilla 4.06 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: CCL Subject: atoms a in specific state Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Since I didn't get much repons on my previous messages to this list, I have rephrased and generalized my question in the hope that this time someone can help me... Are there any programs available that can calculate the density matrix of an atom in a specific state at the SCF and MP2 level of theory? Thanks in advance, Bart. -- Bart Rousseau, Ph.D. student University of Antwerp - Dep. of Chemistry Structural Chemistry - Quantum Chemistry http://sch-www.uia.ac.be/struct/quantum/ From chemistry-request@server.ccl.net Mon Jul 12 13:03:49 1999 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19882 for ; Mon, 12 Jul 1999 13:03:49 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.8.8/jtpda-5.3) with ESMTP id SAA23688 ; Mon, 12 Jul 1999 18:57:25 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id SAA04383; Mon, 12 Jul 1999 18:54:03 +0200 Date: Mon, 12 Jul 1999 18:54:03 +0200 Message-Id: <199907121654.SAA04383@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: CHEMISTRY@ccl.net Subject: Wanted: Heme parameters for Amber 94 force field Dear CCLers, I am looking for heme parameters compatible with the all-atom Amber 94 force fields. All the references I could find (including the CCL archives) are for the older united-atom force field or for OPLS. Is there really nothing for Amber 94? -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Jul 12 14:57:27 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20957 for ; Mon, 12 Jul 1999 14:57:26 -0400 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id LAA29330 for ; Mon, 12 Jul 1999 11:51:03 -0700 (PDT) Date: Mon, 12 Jul 1999 11:51:02 -0700 (PDT) From: "Dale A. Braden" Reply-To: "Dale A. Braden" To: cclpost Subject: Update: plotting MO contours Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Since posting my summary about making black-and-white MO contour plots >from Gaussian98 output data (or .cube file or whatever), I got several additional responses, two of which were particularly helpful in allowing me to actually create such plots. If anyone is interested in a way to do this, I offer one method below. Again, thanks to all who responded. A few respondents pointed out that black-and-white plots are automatically created simply by printing to a black-and-white printer. In my experience, the grayscale that results from such an action is not of publishable quality. Distinguishing the positive and negative phase of the contours is best done, I think, using different line types (solid, dashed, etc.) and thus the ability to control the line type of each individual contour, as well as its value, is important. In this respect, most plotting programs fail. One can use the Gaussian cubegen utility or cube=cards keyword to generate a contour slice through the cube (assuming that the slice you want is parallel to one face of the cube). Do this by taking one step of zero length in one of the directions (you have to take one step or the program will crash). Thanks to Timm Lankau for this idea. A single-line awk script will then convert the multi-column data into 1-column data which can be read by a freeware program called Plotmtv (thanks to Iraj Daizadeh for this suggestion) which can be obtained, among MANY places, from http://csep2.phy.ornl.gov/csep/PLOTMTV/PLTMTV1.html. This program is easy to use and, unlike gnuplot, allows one to control the style of individual contour lines. Plotmtv will output a graphical screen image, and a postscript file. Best wishes to all, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu