From chemistry-request@www.ccl.net Tue Nov 3 03:32:28 1998 Received: from rzusuntk.unizh.ch (rzumail1.unizh.ch [130.60.128.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA08855 Tue, 3 Nov 1998 03:32:27 -0500 (EST) Received: [from rzurs10.unizh.ch (toukie@rzurs10.unizh.ch [130.60.68.60]) by rzusuntk.unizh.ch (8.8.5/SMI-5.25) with ESMTP id JAA25723; Tue, 3 Nov 1998 09:32:26 +0100 (MET)] Received: (from toukie@localhost) by rzurs10.unizh.ch (AIX4.2/UCB 8.7/8.7) id JAA101642; Tue, 3 Nov 1998 09:32:25 +0100 (MET) From: "Dr. S. Shapiro" Message-Id: <199811030832.JAA101642@rzurs10.unizh.ch> Subject: CCL:? re Babel 1.6 for DOS (fwd) To: chemistry@www.ccl.net Date: Tue, 3 Nov 1998 09:32:24 +0100 (MET) Cc: toukie@zui.unizh.ch X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Forwarded message: From chemistry-request@www.ccl.net Thu Oct 8 22:41:23 1998 X-Authentication-Warning: www.ccl.net: ccl set sender to chemistry-request@www.ccl.net using -f Message-Id: <3.0.3.32.19981007131423.00689a80@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 07 Oct 1998 13:14:23 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: CCL:? re Babel 1.6 for DOS Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Sender: chemistry-request@www.ccl.net Errors-To: ccl@ccl.net Precedence: bulk X-Status: X-Keywords: X-UID: 609 Dear Colleagues; After a MOPAC 6.0 run, I obtained a MOPAC.out file and a MOPAC.arc file. I would like to know if there is a way of converting either of these structural files to the Sybyl .mol2 format using Babel 1.6 for DOS that would _also_ incorporate the Mulliken partial atomic charges into the Sybyl .mol2 output? Any suggestions as to whether this is possible, and (if so) what is the relevant command line? Thanks, S. Shapiro toukie@zui.unizh.ch --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From chemistry-request@www.ccl.net Tue Nov 3 05:04:49 1998 Received: from euler.central.cranfield.ac.uk (euler.central.cranfield.ac.uk [138.250.48.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA09037 Tue, 3 Nov 1998 05:04:48 -0500 (EST) Received: from farm1.central.cranfield.ac.uk ([138.250.48.3]) by euler.central.cranfield.ac.uk with smtp (Exim 1.92 #2) for chemistry@www.ccl.net id 0zadKT-0001aP-00; Tue, 3 Nov 1998 10:04:49 +0000 Date: Tue, 3 Nov 1998 10:04:48 +0000 (GMT) From: "R.M.Day" X-Sender: bi0100@farm1.central.cranfield.ac.uk To: chemistry@www.ccl.net Subject: Which is the best technique ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm looking for a bit of advice ! I am attempting to study the conformations of carbohydrates attached to glycohormones, dna etc. We are currently using the GRID search technique implemented in SYBYL for this purpose is this the most reliable approach to find a popular low energy conformation ? Any discussion would be helpful, thanks Richard Day -=-==-=-==-=-=-=-==-==-===-=-= Richard Day Cranfield Biotechnology Cranfield University Bedfordshire MK43 0AL +44 1234 750111 x3563 Home 01462 732192 From chemistry-request@www.ccl.net Mon Nov 2 03:42:01 1998 Received: from kweetal.tue.nl (kweetal.tue.nl [131.155.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA20310 Mon, 2 Nov 1998 03:41:59 -0500 (EST) Received: from sg10.chem.tue.nl [131.155.80.53] by kweetal.tue.nl (8.9.0) for id JAA06729 (ESMTP). Mon, 2 Nov 1998 09:41:58 +0100 (MET) Received: from tgakrh@localhost by sg10.chem.tue.nl (8.8.5) for chemistry@www.ccl.net id JAA04534. Mon, 2 Nov 1998 09:41:58 +0100 (MET) From: Roelant Harmsen Message-Id: <199811020841.JAA04534@sg10.chem.tue.nl> Subject: Basisset for Re To: chemistry@www.ccl.net (Computational Chemistry List) Date: Mon, 2 Nov 1998 09:41:57 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi everyone, I am looking for a DZVP basisset for Rhenium in Dgauss format. Does anyone know where to get one, or does anyone have it? Thanks, Roelant ********************************************************************** Roelant Harmsen |tel: ++31 40 2473575/5032 University of Technology Eindhoven |fax: ++31 40 2455054 Schuit Institute of Catalysis |e-mail: R.J.Harmsen@tue.nl P.O. box 513 |e-mail : tgakrh@chem.tue.nl 5600 MB Eindhoven | The Netherlands |AD&D: Xahnar (Wild Mage) Homepage: http://www.tak.chem.tue.nl/personal/rharmsen ********************************************************************** From chemistry-request@www.ccl.net Mon Nov 2 04:07:06 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA20398 Mon, 2 Nov 1998 04:06:59 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA06046; Mon, 2 Nov 98 16:05:06 -0800 Date: Mon, 2 Nov 1998 16:05:05 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: JOBIN YVON CDMConv Software problem Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I found CDMConv (secondary structure calculation software by JOBIN YVON-SPEX, Instruments S.A.) can not run in PentiumII PC. Did anyone others find same problem? Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@www.ccl.net Tue Nov 3 16:19:59 1998 Received: from cliff.uottawa.ca (root@cliff.uottawa.ca [137.122.6.65]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA28880 Tue, 3 Nov 1998 16:19:58 -0500 (EST) Received: from oreo.science.uottawa.ca (oreo.science.uottawa.ca [137.122.43.15]) by cliff.uottawa.ca (8.8.8/8.8.7) with ESMTP id QAA62442 for ; Tue, 3 Nov 1998 16:19:40 -0500 Received: from OREO/SpoolDir by oreo.science.uottawa.ca (Mercury 1.43); 3 Nov 98 16:19:56 GMT-5 Received: from SpoolDir by OREO (Mercury 1.43); 3 Nov 98 16:19:20 GMT-5 Received: from erik (137.122.43.165) by oreo.science.uottawa.ca (Mercury 1.43); 3 Nov 98 16:19:14 GMT-5 Sender: boufer@uottawa.ca Message-ID: <363F6F0D.41C6@cennas.nhmfl.gov> Date: Tue, 03 Nov 1998 16:01:01 -0500 From: boufer Organization: None X-Mailer: Mozilla 2.02 (X11; I; AIX 1) MIME-Version: 1.0 To: "Comp. Chem. List" Subject: Technical Question : Running G92 on SGI work station Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings all, I am running G92 on a SGI work station. For a geometry optimization, I am only getting 18 to 30%~(checked with top command)of CPU when link l502 is executed although I am the only user connected and running a job. I would appreciate receiving your comments~(past experience ...) Thanks for your time and help. From chemistry-request@www.ccl.net Tue Nov 3 17:41:05 1998 Received: from mx3.cso.uiuc.edu (mx3.cso.uiuc.edu [128.174.5.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA05574 Tue, 3 Nov 1998 17:41:04 -0500 (EST) Received: from london.ks.uiuc.edu (london.ks.uiuc.edu [130.126.120.11] (may be forged)) by mx3.cso.uiuc.edu (8.8.8/8.8.8) with ESMTP id QAA11113 for ; Tue, 3 Nov 1998 16:40:36 -0600 (CST) Received: from jerusalem.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2) id AA014252834; Tue, 3 Nov 1998 16:40:35 -0600 Received: (from ferenc@localhost) by jerusalem.ks.uiuc.edu (940816.SGI.8.6.9/8.6.9)id QAA00804; Tue, 3 Nov 1998 16:40:33 -0600 Date: Tue, 3 Nov 1998 16:40:33 -0600 Message-Id: <199811032240.QAA00804@jerusalem.ks.uiuc.edu> From: Ferenc Molnar To: CHEMISTRY@www.ccl.net Subject: gold surface parameters Dear all: A while ago I posted a message about parameters for the modeling of gold surfaces: > > I would appreciate very much pointers to procedures > for parametrizing the interaction of organic molecules > with gold-surfaces (not parametrization in general!). > Has anybody done MD or MC > simulations on these or similar systems? > > A preliminary literature search did not result in too > many useful references ... Thanks to Pat Hogue and Jeffrey Nauss for their replies: > There was an interesting article in the October issue of Laser Focus World > (p15) describing the self-assembly of an organosulfur compound onto gold > surfaces. The work was done by Elias Greenbaum, Ida Lee, and James Lee at > Oak Ridge National Laboratory. Perhaps one of them can help you. The used > the modified gold surface as a means to immobilize a photosynthetic receptor > component for current-voltage measurements. It is an interesting article. > > > Pat Hogue > Materials and Processes Engineering > Honeywell Satellite Systems Operation > Glendale, AZ 85308 > (602) 561-3748 > > You might want to look into "Molecular Structure of Monolayers from > Thiol-Terminated Polyimide Model Compounds on Gold. Part II: Molecular > Dynamics Simulations", Z. Zhang, T.L. Beck, J.T. Young, and F.J. Boerio, > Langmuir, 1996, 12, 1227-1237. > > > -- > Jeffrey L. Nauss, PhD Phone: (619) 799-5555 > Product Specialist, Simulations Fax: (619) 458-0136 > Molecular Simulations Inc. E-mail: jnauss@msi.com > 9685 Scranton Road > San Diego, CA 92121 The literature search gave the following results: AUTHOR(s): Majid, I. Bristowe, P.D. TITLE(s): An X-ray diffraction and computer simulation study of [111] twist boundaries in gold. In: Philosophical magazine a. physics of condensed JUL 01 1992 v 66 n 1 Page: 73 AUTHOR(s): Chen, C.-C. Paithankar, D.Y. Talbot, J. TITLE(s): Molecular dynamics simulation of gold cluster collisions. In: Zeitschrift fur physik. d, 1993 v 26 supp Page: S165 AUTHOR(s): Terui, Y. Hirokawa, K. TITLE(s): Fourier transform infrared emission spectra of p-nitrobenzoic acid enhanced by island structures of gold: experimental and simulation. In: Vibrational spectroscopy. MAR 01 1994 v 6 n 3 Page: 315 AUTHOR(s): Phillpot, S.R. TITLE(s): Reconstruction of grain boundaries in copper and gold by simulation. In: Journal of materials research. MAR 01 1994 v 9 n 3 Page: 582 SICI Code: 0884-2914(19940301)9:3L.582:RGBC;1- AUTHOR(s): Kubo, M. Stirling, A. Miyamoto, A. TITLE(s): Molecular dynamics simulation for ultrafine gold particles deposited on metal oxides. In: Catalysis today. APR 25 1997 v 36 n 1 Page: 143 Takano, J.-i., Takai, O. , Doyama, M. "Simulation of atomic-scale surface migration in homoepitaxial growth using embedded-atom method potentials for gold. " In: Thin solid films. APR 15 1998 v 318 n 1 / 2 Page: 52 Cheers, Ferenc -- Ferenc Molnar ---------------------------------------------- Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL, 61801, USA Telephone (217) 244-1855 Telefax (217) 244-6078 e-mail ferenc@ks.uiuc.edu http://www.ks.uiuc.edu/~ferenc ---------------------------------------------- In so far as quantum mechanics is correct, chemical questions are problems in applied mathematics. -- Eyring, Walter, & Kimball, 1944 From chemistry-request@www.ccl.net Tue Nov 3 22:27:50 1998 Received: from chu.Chem.nthu.edu.tw (Chu.Chem.nthu.edu.tw [140.114.45.233]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA06734 Tue, 3 Nov 1998 22:27:10 -0500 (EST) Received: by chu.Chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA13861; Wed, 4 Nov 1998 10:10:07 +0800 From: lin@chu.Chem.nthu.edu.tw (Chiu-Ling Lin) Message-Id: <9811040210.AA13861@chu.Chem.nthu.edu.tw> Subject: Spin Density Program? To: CHEMISTRY@www.ccl.net Date: Wed, 4 Nov 1998 10:10:06 +0800 (TAIST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear Netters, Can anyone suggest a program package, from which one may obtain the spin density on different atoms in a molecular system? Thanks a lot in advance. Hon-Wei Wan