From chemistry-request@server.ccl.net Wed Jul 24 17:34:14 2002 Received: from localhost.localdomain ([130.67.56.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OLYCr01906 for ; Wed, 24 Jul 2002 17:34:12 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by localhost.localdomain (8.11.6/8.11.6) id g6OLYYL18456 for chemistry@ccl.net; Wed, 24 Jul 2002 23:34:34 +0200 Content-Type: text/plain; charset="us-ascii" From: Sergio To: CCL Subject: STC Date: Wed, 24 Jul 2002 23:34:34 +0200 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200207242334.34261.sergio@proinformatix.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6OLYEr01907 Hello, have anyone here used STC ? I am trying to calculate the thermodynamics between two associated protein bodies, but get this error in the log file. ************************************************ Fatal Error Detected! Module.: proc_bound Message: Amino acid inconsistency: GLY --> 2 698 LEU N 13.9683 ************************************************ Thanks! Sergio From chemistry-request@server.ccl.net Thu Jul 25 09:50:06 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g6PDo6Y31458 for chemistry@ccl.net; Thu, 25 Jul 2002 09:50:06 -0400 Message-Id: <200207251350.g6PDo6Y31458@server.ccl.net> Date: Thu, 25 Jul 2002 17:32:41 +0900 From: "Chan Kyung Kim" To: chemistry@ccl.net Subject: Computational Chiral Chromatography Dear Computational Chemists: One of the Ph. D. student in my department asked me if it is possible to do computational study on the chiral chromatography. He wanted to know the separability of R,S isomers with fixed stationary phases. I found that "Molecular Mechanics across Chemistry" has a section on this topic. It reads "With the center of mass for the analyte determined in terms of r, theta, pi there are three degrees of freedom left for a rigid analyte. These degrees of freedom are described in terms of three Euler angles of rotation. Lipkowitz et al. established a grid of theta and pi angles, varied r to minimize van der Waals contacts, and evaluated the intermolecular energy over a set of 1020 Euler angles. The set of 1020 configurations were....." I think there might be some program available to do this kind of works. Would you please tell me where I can get such programs or information? He also wants to know if this kind of computational studies can be done in mixed solvents environment. I would like to hear your opinion. Thank you for your time. With best wishes, Chan. =============================================================================== Prof. Chan Kyung Kim Department of Chemistry Inha University Inchon, 402-751, Korea (Tel) +82-32-860-7684 (Fax) +82-32-867-5604 (email) kckyung@inha.ac.kr From chemistry-request@server.ccl.net Thu Jul 25 12:16:37 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 g6PGGar04386 for ; Thu, 25 Jul 2002 12:16:36 -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 g6PHCKp11998 for ; Thu, 25 Jul 2002 19:12:20 +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 SAA17558; Thu, 25 Jul 2002 18:12:18 +0200 (METDST) Date: Thu, 25 Jul 2002 18:12:17 +0200 (METDST) From: Marcin Krol To: chemistry@ccl.net Subject: Merz-Kollman charges - constraints Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers I'm using MK charge fitting scheme as impl;emented in Gaussian98 for a symmteric molecule. However, charges, which should be equivalent, differ for about 0.1e. Increasing number of points doesn't help. Do you know of any program which would constrain charges on equivalent atoms before the fit (like in RESP or CHELP-BOW methods)? Or maybe Gaussian can do it? I know, I could average the charges after the fit but it is not a very good idea, I suupose. Thank you in advance for answers. sincerely Marcin Krol From chemistry-request@server.ccl.net Thu Jul 25 15:55:59 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6PJtxr11441 for ; Thu, 25 Jul 2002 15:55:59 -0400 Received: through eSafe SMTP Relay 1026991842; Thu Jul 25 15:49:08 2002 Received: from mindless.com (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id PAA23850 for ; Thu, 25 Jul 2002 15:55:58 -0400 (EDT) Message-ID: <3D4057CC.E29CA321@mindless.com> Date: Thu, 25 Jul 2002 15:55:56 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: open source relaxation softwear Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello fellow cclers I have a simple question for everyone. Does anyone know of any simple, open source (free) software that can be used to do a simple relaxation on a pdb molecule? Or are there any internet sites that do this remotely. I need something with binaries for windows. It only needs to do a very simple molecular mechanics relaxation. Thanks for your response. David Smith From chemistry-request@server.ccl.net Thu Jul 25 17:03:55 2002 Received: from zephyr.meteo.McGill.CA ([132.206.43.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6PL3sr13851 for ; Thu, 25 Jul 2002 17:03:54 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA23572; Thu, 25 Jul 2002 16:55:02 -0400 Date: Thu, 25 Jul 2002 17:03:50 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.53d) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <13411658373.20020725170350@zephyr.meteo.mcgill.ca> To: CCL Subject: Programs for drawing the molecular structure for papers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers What programs do you use for representing geometry parameters of the molecules in papers? A program of this kind have to plot a molecular structure in black&white (not gray) as ball&sticks and if it's possible to print bond lengths and angles. Thank you and best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. ---------------------------------------------------------------- E-mail: Andrew@Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com