From chemistry-request@server.ccl.net Thu Aug 22 05:40:42 2002 Received: from real.cyf-kr.edu.pl ([149.156.2.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7M9egQ20341 for ; Thu, 22 Aug 2002 05:40:42 -0400 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by real.cyf-kr.edu.pl (8.11.6/8.11.6) with ESMTP id g7M9a2q24512 for ; Thu, 22 Aug 2002 11:36:02 +0200 X-RAV-AntiVirus: This e-mail has been scanned for viruses on host: real.cyf-kr.edu.pl Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id LAA10164; Thu, 22 Aug 2002 11:35:47 +0200 (METDST) Date: Thu, 22 Aug 2002 11:35:44 +0200 (METDST) From: Marcin Krol To: chemistry@ccl.net Subject: CHARMM - inserting ions (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I wonder if there is a simple method to make charmm insert ions to a box of a solvated macromolecule? I have searched the web but found no scripts that could add ions automatically (preferably in the region of maximal or minimal electrostatic potential (electrostatic energy)) in CHARMM. How could I print out electrostatic energy of each atom (residue) in charmm? I tried to load electrostatic energy into WMAIN, but failed. Thanks for any clues Marcin Krol From chemistry-request@server.ccl.net Thu Aug 22 09:29:27 2002 Received: from ws0e.pc.chemie.tu-darmstadt.de ([130.83.242.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7MDTQQ27578 for ; Thu, 22 Aug 2002 09:29:27 -0400 Received: from localhost (hatice@localhost) by ws0e.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id PAA13452 for ; Thu, 22 Aug 2002 15:29:21 +0200 (CDT) Date: Thu, 22 Aug 2002 15:29:20 +0200 From: "Dr. Hatice Can" To: chemistry@ccl.net Subject: Convert G98 output file to pdb Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, I need to convert my Gaussian98 output file to the pdb file which can be readable by sybyl or other programs.If you could sent to me any scripts or free programs, I will be glad. Thank you in advance. Regards Hatice ***************************************************************************** Dr. Hatice Can Darmstadt University of Technology Chemistry Department Physical Chemistry I Petersenstrase 20 64287 Darmstadt Germany Phone: (+49) 6151 16 5397 Fax: (+49) 6151 16 4298 E-mail: hatice@pc.chemie.tu-darmstadt.de WWW: http://www.pc.chemie.tu-darmstadt.de/staff/hatice/ ***************************************************************************** From chemistry-request@server.ccl.net Wed Aug 21 17:45:45 2002 Received: from rhodent.usask.ca ([128.233.48.136]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7LLjjQ23751 for ; Wed, 21 Aug 2002 17:45:45 -0400 Received: from pc.chemie.tu-darmstadt.de (localhost.localdomain [127.0.0.1]) by rhodent.usask.ca (8.11.6/8.11.6) with ESMTP id g7LLdnK06233 for ; Wed, 21 Aug 2002 15:39:49 -0600 Sender: thomas@localhost.localdomain Message-ID: <3D6408A4.4FA080DA@pc.chemie.tu-darmstadt.de> Date: Wed, 21 Aug 2002 15:39:48 -0600 From: Thomas Exner X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.8-34.1mdksmp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary of "rotating a density matrix" Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, I have an additional question to the rotation of the density matrix. I accounted some difficulties while implementing the rotation of the d orbitals as discribed by Ferre et al. (J.Comp.Chem. 23(6) 2002, 610-624) and Philipp and Friesner (J.Comp.Chem. 20(14) 1999, 1468-1494). I think I found one error in the equation in the second paper. But because I don't really understand how the rotation matrix is affiliated, it is impossible for me to figure out if there are any other errors in the equation or if it is a problem with my implementation. I would appriciate if someone could give me some hints how the rotation matrix has to be constructed. Perhaps, this could also help me to construct a rotation matrix for f orbital. Thank you very much. Best wishes, Thomas -- ____________________________________________________________________ Dr. Thomas Exner Computational, Theoretical & Mathematical Chemistry Department of Chemistry University of Saskatchewan 110 Science Place 431 Edmund Park Saskatoon, SK, S7N 5C9 Saskatoon, SK, S7H 0Z4 Canada Canada phone: +1-306-966-5357 +1-306-382-5397 fax: +1-306-966-4730 Department of Physical Chemistry Physical Chemistry I Darmstadt University of Technology (TUD) Petersenstr. 20 Auf der Marienhoehe 5 64287 Darmstadt 64297 Darmstadt Germany Germany phone: +49-6151-16 2398 +49-6151-537165 fax: +49-6151-16 4298 e-mail: exner@pc.chemie.tu-darmstadt.de texner@gmx.net WWW: http://www.pc.chemie.tu-darmstadt.de/staff/exner/ ____________________________________________________________________ From chemistry-request@server.ccl.net Thu Aug 22 01:23:49 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7M5NmQ13849 for ; Thu, 22 Aug 2002 01:23:49 -0400 Received: from [24.65.168.211] ([24.65.168.211]) by cascara.uvic.ca (8.12.4/8.12.4) with SMTP id g7M5NfJE223128 for ; Wed, 21 Aug 2002 22:23:42 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: identifying single configuration systems Date: Wed, 21 Aug 2002 22:23:50 -0700 Message-ID: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos v3.59 X-Scanned-By: MIMEDefang 2.16 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7M5NnQ13850 All Is it possible to tell, a priori, if a system can be reasonably and reliably represented by a single configuration method? Are there any systems that generally fail? transition states, partially filled orbitals, partially filled _degenerate_ orbitals, etc. Thanks, Roy Jensen From chemistry-request@server.ccl.net Wed Aug 21 21:44:55 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7M1isQ09015 for ; Wed, 21 Aug 2002 21:44:55 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g7M1rYF24707 for chemistry@ccl.net; Wed, 21 Aug 2002 18:53:34 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g7M1rYf24698 for ; Wed, 21 Aug 2002 18:53:34 -0700 To: chemistry@ccl.net Subject: Accelrys Macromolecular Modeling Workshops in Europe in the Fall MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Wed, 21 Aug 2002 18:44:36 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 08/21/2002 06:44:39 PM, Serialize complete at 08/21/2002 06:44:39 PM Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7M1itQ09016 Accelrys Inc. will be holding eight customer-training workshops for macromolecular modeling in Europe in the fall of 2002. Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php. Further detailed information about Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html). We start off 1-4 October in Modena, Italy, where the workshops "Introduction to Life Science Modeling with InsightII" and "Structure-Based Drug Design with InsightII" will be offered at the CICAIA, Universita` di Modena e Reggio Emilia. > From 8-9 October, the "Introduction to Life Science Modeling with InsightII" workshop will be offered again but in our office in Munich, Germany. Following that course, we will offer the "Macromolecular X-ray Structure Determination" workshop, also in Munich. This second workshop will focus on X-ray crystallography tools in QUANTA and CNX. In our office in Cambridge, UK, from 29 October to 1 November, Accelrys will be holding a pair of workshops focusing on NMR techniques. The "Biomolecular NMR: Processing and Analysis Workshop" will be held 29-30 October and focuses on using FELIX. On 31 October - 1 November, the "Biomolecular NMR: Structure Determination Workshop" will be given. This course addresses the generation, refinement, and evaluation of structures based upon NMR data predominantly using NMR X-PLOR in InsightII and CNX. Finally, in Paris from 5-8 November, we will offer the "Introduction to Life Science Modeling with InsightII" and "Homology-Based Protein Design" workshops. The classes will be held at Uiversité Pierre et Marie Curie, Salle de Modelisation et de l'Imager. Fees for each two-day course outside the UK are EUR1350 commercial, EUR1020 government/nonprofit, and EUR750 academic. For courses held in the UK, the fees are GBP830 commercial, GBP630 government/nonprofit, and GBP460 academic. Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php. Further detailed information about these and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Elizabeth Crookenden +44 (0) 1223 228691 Jeffrey L. Nauss +1 858 799 5555 -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Wed Aug 21 13:24:13 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7LHODQ15646 for ; Wed, 21 Aug 2002 13:24:13 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA15888; Wed, 21 Aug 2002 13:24:12 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3D63BEC1.1D0756C3@cornell.edu> Date: Wed, 21 Aug 2002 12:24:33 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: a Rasmol question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I have a question about Rasmol. I use a version of Rasmol (RasWin, actually to be more correct) that came with the package Chem2Pac. It's really nice and easy to use to visualize structures. Unfortunately, it neglects to draw bonds sometimes. Is there a way to manually draw a bond between two atoms that are supposed to be bonded? Thanks in advance. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853