From hurst@hyper.hyper.com Fri Jun 10 00:24:45 1994 Received: from seraph.uunet.ca for hurst@hyper.hyper.com by www.ccl.net (8.6.4/930601.1506) id AAA07940; Fri, 10 Jun 1994 00:16:53 -0400 Received: from hyper by mail.uunet.ca with UUCP id <111191-4>; Fri, 10 Jun 1994 00:04:36 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ccl.net!chemistry) id AA12108; Thu, 9 Jun 94 17:28:32 -0400 Date: Thu, 9 Jun 1994 17:28:32 -0400 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9406092128.AA12108@hyper.hyper.com.hyper.com> To: xiang@auriga.rose.brandeis.edu (Xiaoou Xiang), chemistry@ccl.net Subject: Re: CCL:Monte Carlo,again... Phil Xiang asks: > Let me be more specific. I want to use Monte Carlo method to sample the > conformational space of a small drug molecule to find the global and local > minima. The molecular mechanics programs I have are AMBER and CHARMM, none of > which came with Monte Carlo utility. The combination of HyperChem and ChemPlus can be used for Monte Carlo conformational searches for low energy conformations, using MM+ (extension of MM2), AMBER, CHARMM, or OPLSA molecular mechanics force fields or CNDO, INDO, INDO/1, INDO/S, MINDO/3, MNDO, AM1 or PM3 semi-empirical quantum mechanics to define the potential surface. For rings it uses the TFLEX algorithm of Istvan Kolosovary and Wayne Guida, and has no software limitations on the number of torsions that can be varied. There are several options for search methodology and testing for duplication of conformations (including automatically determining equivalent atom orderings). They are both commercial products (academic prices for HyperChem and ChemPlus are US$ 995 and US$ 495 respectively) that run on PCs with Windows, and I have a very vested interest - I wrote the conformational search module in ChemPlus and have been a HyperChem developer since '88! To get more info, send email to info@hyper.com. In the DOS/Windows world there are two other programs I can think of that might fulfill your need. One that has been advertised recently is PowerSearch by Tripos, which uses the Tripos force field and I don't think that it can handle rings. I think that PC Model by Serena can also do Monte Carlo conformational searches, using their MMX force field. Hope this helps, Graham Hurst ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com From savary@sc2a.unige.ch Fri Jun 10 04:24:51 1994 Received: from chx400.switch.ch for savary@sc2a.unige.ch by www.ccl.net (8.6.4/930601.1506) id DAA09023; Fri, 10 Jun 1994 03:49:33 -0400 X400-Received: by mta chx400.switch.ch in /PRMD=Switch/ADMD=Arcom/C=Ch/; Relayed; Fri, 10 Jun 1994 09:48:57 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Fri, 10 Jun 1994 09:48:47 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Fri, 10 Jun 1994 11:48:34 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Fri, 10 Jun 1994 10:48:34 +0200 Date: Fri, 10 Jun 1994 10:48:34 +0200 X400-Originator: savary@sc2a.unige.ch X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;<01HDDFKB7Y5U004ZHW@uni2b.unige.] X400-Content-Type: P2-1984 (2) Content-Identifier: viewing cryst... Alternate-Recipient: Allowed From: " (Francois Savary)" Message-ID: <01HDDFKB7Y5U004ZHW@uni2b.unige.ch> To: CHEMISTRY@ccl.net Subject: viewing crystals with polyedra X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT X-Sender: savary@sc2a.unige.ch Hello there dear listers, I am looking for some nice pictures of crystals being drawn with polyedra, like for example silicate clusters drawn with bipyramidal polygons having their oxygens at each vertex or supracondutor metals.(need just an example for a speech) Is there somewhere over the net a ftpsite where I could get those images. I know Dietrich and Maigret (J. Mol. Graphics, (1991), Vol.9, p. 85) have developped a program for visualizing inorganic crystals Does someone knows their e-mail? (Iknow this is not the place, sorry) Thanx for any help. Please do e-mail if possible directly to me. Will summarize if there is any interest Francois ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch ---------------------------------------------------------------------------- From ccevc16@cti.csic.es Fri Jun 10 07:24:51 1994 Received: from CTI for ccevc16@cti.csic.es by www.ccl.net (8.6.4/930601.1506) id GAA09985; Fri, 10 Jun 1994 06:31:06 -0400 Received: from cti.csic.es by abeto.cti.csic.es (PMDF V4.2-14 #3407) id <01HDDGLPGAHS00291M@abeto.cti.csic.es>; Fri, 10 Jun 1994 10:17:58 GMT+0200 X400-Received: by mta cti.csic in /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Fri, 10 Jun 1994 10:17:39 UTC+0100 X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Fri, 10 Jun 1994 10:17:39 UTC+0100 Date: Fri, 10 Jun 1994 10:17:39 UTC+0100 From: Victor Cruz Subject: MOPAC93 for DEC-alpha To: chemistry@ccl.net Message-id: <7*ccevc16@cti.csic.es> Content-identifier: 7 Content-transfer-encoding: 7BIT X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;940610101739] X400-Originator: ccevc16@cti.csic.es X400-Recipients: chemistry@ccl.net Hello everybody, This is to locate any individual who has ported MOPAC93 to DEC-alpha running either OpenVMS or OSF/1 . To my knowledge QCPE distributes a Sun version. Thanks in advance. Victor Cruz CTI-CSIC Pinar,19 28006-Madrid,Spain From wriggers@lisboa.ks.uiuc.edu Fri Jun 10 12:25:01 1994 Received: from lisboa.ks.uiuc.edu for wriggers@lisboa.ks.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id LAA13538; Fri, 10 Jun 1994 11:51:27 -0400 Received: by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA21095; Fri, 10 Jun 94 10:51:27 -0500 Date: Fri, 10 Jun 94 10:51:27 -0500 From: Willy Wriggers Message-Id: <9406101551.AA21095@lisboa.ks.uiuc.edu> Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: subscription request Reply-To: Willy Wriggers I would like to be included in the comp chem mailing list. Sincerely, Willy Wriggers ___________________________________________ Beckman Institute and Department of Physics University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL, 61801, USA Telephone (217) 244-2905 Telefax (217) 244-6078 e-mail wriggers@uiuc.edu From mercie@mail.med.cornell.edu Fri Jun 10 14:25:00 1994 Received: from mail.med.cornell.edu for mercie@mail.med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id NAA14684; Fri, 10 Jun 1994 13:50:27 -0400 Received: (from mercie@localhost) by mail.med.cornell.edu (8.6.8/ech1.73) id NAA08816; Fri, 10 Jun 1994 13:50:27 -0400 Date: Fri, 10 Jun 1994 13:50:26 -0400 (EDT) From: Gustavo Mercier Subject: Brownian Dynamics H2O To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am interested in doing Brownian Dynamic Simulations with UHBD along the lines of the work done by McCammon using SOD and superoxide, except that the "substrate" is a water molecule. I would appreciate any info on the following: 1) References to or the value of the hydrodynamic radius of water. 2) Representation of water for brownian dynamic simulations. Further work by McCammon and coworkers on TIM with glyceraldehyde phosphate as a substrate demonstrated that you did not need a full "molecular" description of the substrate, but a simple sphere was inadequate. In their case I believe a two sphere model was successful. Please send messages to me. I will summarize to the NET. thanks gus mercier,jr. mercie@cumc.cornell.edu (notice the absence of the last "e" from my name!) From hero%JPNNDA.bitnet@phem3.acs.ohio-state.edu Fri Jun 10 16:24:57 1994 Received: from phem3 for hero%JPNNDA.bitnet@phem3.acs.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id QAA16825; Fri, 10 Jun 1994 16:03:27 -0400 From: Received: from JPNSUT00.BITNET (MAILER@JPNSUT00) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HDDSMYR12O99OVG4@phem3.acs.ohio-state.edu>; Fri, 10 Jun 1994 16:02:35 EDT Received: from JPNSUT00 by JPNSUT00.BITNET (Mailer R2.10 ptf000) with BSMTP id 4336; Sat, 11 Jun 94 05:01:37 JST Received: from JPNNDA.BITNET by JPNSUT00.BITNET (Mailer R2.10 ptf000) with BSMTP id 4334; Sat, 11 Jun 94 05:01:36 JST Received: by cmmail.nda.ac.jp (5.67+1.6W/SMI-4.1) id AA13494; Sat, 11 Jun 94 05:02:08 JST Received: from cmr4w1.nda.ac.jp (cmr4w1) by cmmail.nda.ac.jp (5.67+1.6W/SMI-4.1) id AA13489; Sat, 11 Jun 94 05:02:07 JST Received: by cmr4w1.nda.ac.jp; id AA06525; Sat, 11 Jun 1994 05:02:49 +0900 Received: by cmr4w1.nda.ac.jp; id AA06521; Sat, 11 Jun 1994 05:02:48 +0900 Received: by cmr1w1.nda.ac.jp; id AA03440; Sat, 11 Jun 1994 05:02:48 +0900 Date: Sat, 11 Jun 1994 05:02:47 +0900 Subject: Re: polymer chemistr list In-reply-to: Your message of "Mon, 06 Jun 94 21:56:31 EST." <9406062156.AA09772@vigyan.iisc.ernet.in> To: CHEMISTRY@ccl.net Message-id: <9406102002.AA03440@cmr1w1.nda.ac.jp> Content-transfer-encoding: 7BIT X-Mts: smtp On Mon, 06 Jun 1994 21:56:31 -0500 (Mon) In article <9406062156.AA09772@vigyan.iisc.ernet.in> ipcakc@vigyan.iisc.ernet.in said: >> Is there anything like "Ploymer Chemistry List" as we have >> computational chemistry list? If you are interested in Polymer Physics, would you add to the Polymer Physics Discussion List? To subscribe this list, send the messege "subscribe polymerp firstname lastname" to listserv@rutvm1.rutgers.e du. Hiroki KIMOTO Department of Chemistry, National Defense Academy, 10-20 Hashirimizu 1-chome, Yokosuka, JAPAN Internet : SDI00673@niftyserve.or.jp or TCC00356@niftyserve.or.jp BITNET : hero%jpnnda.bitnet@cunyvm.cuny.edu