From chemistry-request@server.ccl.net Tue Jun 8 02:44:59 1999 Received: from LMSMRM ([202.127.25.133]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA01334 for ; Tue, 8 Jun 1999 02:44:37 -0400 Received: from LMSMRM (localhost [127.0.0.1]) by LMSMRM (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA01176 for ; Tue, 8 Jun 1999 14:20:49 +0900 Sender: user@iris.sipp.ac.cn Message-ID: <375CA830.41C6@iris.sipp.ac.cn> Date: Tue, 08 Jun 1999 14:20:48 +0900 From: maoxiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: questions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone: Are there some of you can give me some suggestions about the input Z-matrix for GAMESS-UK, I am doing some transition search with it. But sometimes I will met the error like the following:(error detected in converting z-matrix to cartesian coordinate). I reprepare the input Z-matrix to set the dummy atom and half angle in the input file, and I still met the problem. So would you please tell me if there are some good methods or some softwares( free of charge) that I can set the proper Z-matrix( to set dummy atom automaticlly). Another question is in the transtion search, for example, if I want to model the cleavage of some bonds, should I give a long bond length of the reacting bond,because the input file should be the reasonable estimate of the TS structure. Am I right. Hope to hear from you soon. Regards, Mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Jun 8 06:59:53 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA04136 for ; Tue, 8 Jun 1999 06:59:50 -0400 Message-Id: <199906081059.GAA04136@server.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Tue, 08 Jun 1999 09:50:56 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@ccl.net Date: Tue, 8 Jun 1999 11:53:01 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: Tinker and benzene deriv. Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Xavier Fradera wrote > Hi, > > a few days ago, I asked for a program that could convert sybyl atom types to MM2 or other force- > fields for use in tinker. A. Stevens and C. Gonzalez suggested using the Babel program. > > I have tried babel-1.6. It can read sybyl mol2 fields and write MM2, MM3 and tinker input files, > among other. However, I am not absolutely sure that the atom type conversion is done adequately. > For instance, I have tried translating a mol2 file for a small molecule (benz.mol2) to a tinker > file (benz.xyz) (files are at the end) The atom types generated for a tinker output coincide with > those generated for MM2 and MM3, so i tried running tinker single-point energy calculations using > the MM2, MM3 and tinker parameter sets. In all cases, tinker fails to calculate the energy because > it finds bonds (and torsions) for which it has no parameters, e.g., for the MM2 force-field: > > Undefined Bond Stretching Parameters : > > Type Atom Names Atom Classes > > Bond 1-C 7-C+ 2 30 > Bond 7-C+ 8-N 30 9 > Bond 7-C+ 9-N 30 9 Dear Xavier, I am not a great expert in Tinker, but I as far as I know, Tinker is parametrized specially for proteins. Therefore it is understandable that it lacks parameters in the case of other type of compounds, when it tries to assignate the force field atom types. The xmol type xyz file, which was at the end of your letter, does not contain any info about force field atom types, it contains only elemental symbols and the coordinates and connections. You should try other force field representations, or obtain the missing parameters from the literature. Unfortunately, this happens quite often with "exotic" molecules. best regards tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ From chemistry-request@server.ccl.net Tue Jun 8 12:17:58 1999 Received: from argyle.richmond.edu (argyle.richmond.edu [141.166.97.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA09013 for ; Tue, 8 Jun 1999 12:17:58 -0400 Received: from Chem155.richmond.edu (ur060109.richmond.edu [141.166.60.109]) by argyle.richmond.edu (8.9.0/8.9.0) with SMTP id MAA24011; Tue, 8 Jun 1999 12:11:51 -0400 (EDT) Message-Id: <1.5.4.32.19990608161222.006ac608@student.richmond.edu> X-Sender: jmiller5@student.richmond.edu X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 08 Jun 1999 12:12:22 -0400 To: help@gaussian.com, fparnold@rainbow.uchicago.edu, dmpotts@rainbow.uchicago.edu, chemistry@ccl.net From: Jennifer Miller Subject: CCL: symmetry restrictions on gaussian Cc: sabrash@richmond.edu I am trying to run a gaussian job at a symmetry lower than the highest available symmetry. We know that we need to set IOp(4/9=200 and 2/19=symmetry in a hollerith string) but we don't know what the hollerith string for C2V is. Nor is it apparent from the Gaussian manuals. Can anyone help us? Best regards, Jennifer Miller From chemistry-request@server.ccl.net Tue Jun 8 12:23:49 1999 Received: from usintout02 (usintout02.bms.com [165.89.129.232]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA09237 for ; Tue, 8 Jun 1999 12:23:49 -0400 Received: from nsusmsg02.net.bms.com ([165.89.129.50]) by mochilla.bms.com (PMDF V5.2-31 #38482) with ESMTP id <0FD000F5RNW4Z7@mochilla.bms.com> for chemistry@ccl.net; Tue, 8 Jun 1999 16:16:52 +0000 (GMT) Received: from bms.com ([140.176.5.127]) by nsusmsg02.net.bms.com (Netscape Messaging Server 3.6) with ESMTP id AAA64F4 for ; Tue, 08 Jun 1999 16:16:51 +0000 Date: Tue, 08 Jun 1999 12:16:42 -0400 From: John S Tokarski Subject: hydrogen bonds involving cysteine To: chemistry@ccl.net Message-id: <375D41EA.A08E5FFE@bms.com> Organization: Bristol-Myers Squibb MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en]C-BMY (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear netters, Has anyone observed a cysteine -SH hydrogen bond to an sp2 oxygen? Thanks in advance, John From chemistry-request@server.ccl.net Tue Jun 8 12:50:06 1999 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA09566 for ; Tue, 8 Jun 1999 12:50:05 -0400 Received: from ce.fis.unam.mx ([132.248.33.121]) by ce.fis.unam.mx with ESMTP (8.7.1/8.7.1) id LAA03567 for ; Tue, 8 Jun 1999 11:38:01 -0700 (PDT) Message-ID: <375D5680.B99C798B@ce.fis.unam.mx> Date: Tue, 08 Jun 1999 11:44:32 -0600 From: Max Valdez Organization: Centro de Ciencias Fisicas, UNAM X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:Tinker and benzene deriv. References: <199906081059.GAA04136@server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Everybody: I have the same problem that Tamas Gunda has, I would any info on new programs to treat "exotic molecules", it has been a headache trying every program Ii found and with none of it I've been able to calculate anything because of the lack of some parameter. Would it be possible that someone has parameters for MM2 or MM3 for tinker or any other program like it?? Best Regards Max Valdez From chemistry-request@server.ccl.net Mon Jun 7 23:33:26 1999 Received: from pplas.icas.ac.cn (root@pplas.icas.ac.cn [159.226.64.137]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA28589 for ; Mon, 7 Jun 1999 23:33:14 -0400 Received: from yangjy.pplas.icas.ac.cn ([159.226.86.72]) by pplas.icas.ac.cn (8.8.7/8.8.7) with SMTP id XAA00639 for ; Mon, 7 Jun 1999 23:26:15 +0800 Message-Id: <3.0.32.19990608112926.0068a478@159.226.86.106> X-Sender: ychen@159.226.86.106 (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 08 Jun 1999 11:29:26 +0800 To: chemistry@ccl.net From: Yantao Chen Subject: spectral study on protein-ligand complexes Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Sirs: If you have a list of references of the spectral study on the protein-ligand complexes, including NMR, IR, MS..., I will appreciate if you could send me this important information. Thank you very much. Best regards, Yantao Chen ********************************** Yantao Chen, Ph. D. Group 507, Institute of Chemistry Chinese Academy of Sciences P.O. Box 2709, Beijing 100080 P. R. China Fax: +86-10-62559373 Email: ychen@pplas.icas.ac.cn ********************************** From chemistry-request@server.ccl.net Tue Jun 8 12:02:37 1999 Received: from pakistanmail.com (root@pakistanmail.hypercon.com [198.64.247.68]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA08689 for ; Tue, 8 Jun 1999 12:02:35 -0400 From: peghaam@pakistanmail.com Received: from pakistanmail.com ([198.64.247.68]) by pakistanmail.com ; Tue, 08 Jun 1999 15:52:42 -0000 Sender: peghaam@pakistanmail.com Reply-to: peghaam@pakistanmail.com To: chemistry@ccl.net Date: Tue, 8 Jun 1999 15:52:42 GMT Subject: Biophysics course Message-id: <375d3c4a.2f1f.0@pakistanmail.com> X-User-Info: 203.128.252.8 Dear CCL subscriber I want design an elementary course of Biophysics for 1st. year undergraduate students of Biomedical Engg. Dept. Any help and/or comments in this regards will be highly appreciated. Kamran Azim Uni. of Karachi Karachi Pakistan. _______________________________________________________________________ FREE Sub-Domains! your_name.paklinks.com http://www.paklinks.com/nicks/ Get your free @pakistanmail.com email address http://pakistanmail.com