From AA@CHEM.UNI.WROC.PL Tue Sep 13 04:49:08 1994 Received: from sun1000.ci.pwr.wroc.pl for AA@CHEM.UNI.WROC.PL by www.ccl.net (8.6.9/930601.1506) id DAA26501; Tue, 13 Sep 1994 03:58:24 -0400 Received: from hera.math.uni.wroc.pl by sun1000.ci.pwr.wroc.pl (5.0/SMI-SVR4) id AA26710; Tue, 13 Sep 1994 09:54:23 --100 Received: from chem.uni.wroc.pl (ichuwr.chem.uni.wroc.pl) by hera.math.uni.wroc.pl (5.0/SMI-SVR4) id AA12966; Tue, 13 Sep 1994 09:54:57 --100 Received: from ICHUWR/SMTPQueue by chem.uni.wroc.pl (Mercury 1.11); Tue, 13 Sep 94 9:58:25 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Tue, 13 Sep 94 9:57:57 +0100 From: "Agnieszka Abkowicz" To: chemistry@ccl.net Date: Tue, 13 Sep 1994 09:57:57 GMT+1 Subject: z-matrix for gamess X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail v3.1 (R1) Message-Id: <12047790FEF@chem.uni.wroc.pl> Content-Length: 124 Dear Netters, Is there a possibility to input data in Gamess by means z-matrix instead of cartesian coordinates? Agnieszka From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From dec@proteus.co.uk Tue Sep 13 10:46:54 1994 Received: from eros.britain.eu.net for dec@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id KAA00663; Tue, 13 Sep 1994 10:13:57 -0400 Message-Id: <199409131413.KAA00663@www.ccl.net> Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Tue, 13 Sep 1994 15:12:47 +0100 From: David Clark Date: Tue, 13 Sep 94 14:16:44 -0100 To: CHEMISTRY@ccl.net Subject: Inverse folding/sequence threading/de novo folding software Dear All Is anyone aware of any available software (commercial or otherwise) for inverse protein folding/sequence threading or de novo folding? I'm aware of TRIPOS' Matchmaker program but would be interested to know of any others. Many thanks David E. Clark From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From berry@ccl.net Wed Aug 17 09:30:00 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA09208; Wed, 17 Aug 1994 09:29:59 -0400 From: "Robby A. Berry" Message-Id: <199408171329.JAA09208@www.ccl.net> Subject: This is a test To: ccl@ccl.net (Computational Chemistry) Date: Wed, 17 Aug 1994 09:29:58 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 374 Status: RO If you are not Jan Labanowski or Rob Berry, you should not be able to see this.If you can, it means something has gone seriously wrong. Please notify berry@ccl.net (Rob Berry). Please do *not* send email to Jan. Thank you, and my apologies. Sincerely, Rob Berry -- berry@ccl.net Resume, PGP public key available via finger. Disclaimer: I speak for nobody but myself. From IQOR1@cc.uab.es Tue Sep 13 10:54:56 1994 Received: from CCUAB1 for IQOR1@cc.uab.es by www.ccl.net (8.6.9/930601.1506) id KAA00574; Tue, 13 Sep 1994 10:08:00 -0400 From: Received: from cc.uab.es by cc.uab.es (PMDF V4.2-15 #2461) id <01HH2IA2YZV48X1DLP@cc.uab.es>; Tue, 13 Sep 1994 16:04:01 GMT+0200 Date: Tue, 13 Sep 1994 16:04:01 GMT+0200 Subject: Anwsers on question on Md on a PC-486 To: chemistry@ccl.net Message-id: <01HH2IA30VDU8X1DLP@cc.uab.es> Organization: Universitat Autonoma de Barcelona X-PS-Qualifiers: /charset=dec-mcs X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Netters, A month ago I ask a question on any software for doing MD on a PC-486. Please find herein the anwsers I got. Yours truly, Carlos JAIME, Univ. Autonoma de Barcelona, Spain. =========================================================================== From: IN%"chris@glycob.ox.ac.uk" 9-AUG-1994 21:08:07.01 Yes, I have AMBER going for a 486 using the Salford 486 compiler. It runs well giving about 10ps per day for a 2000 atom system with a cutoff of 10A. You will have to get the permission of the University of California and Peter Kollman before I can send it to you. *************************************************************** * Dr. Chris. Edge * Tel. +44-865-275-338 * * Glycobiology Institute * Fax. +44-865-275-216 * * Oxford University * e-mail chris@glycob.ox.ac.uk * * South Parks Road * 100117.3646@compuserve.com * * Oxford OX1 3QU U.K. * * *************************************************************** ============================================================================= From: IN%"abby@mercury.aichem.arizona.edu" "Abby Parrill" 10-AUG-1994 00:11:31.79 Have you tried Hyperchem? __________________________________________________________ Abby Parrill Chemistry Department Artificial Intelligence in Chemistry Laboratory The University of Arizona abby@mercury.aichem.arizona.edu __________________________________________________________ ============================================================================= From: IN%"frits@rulglj.LeidenUniv.nl" 10-AUG-1994 11:04:11.89 Put Linux on your PC-486 and compile all freely available UNIX MD programs? mail me back for more info :-) Greetings, Frits Daalmans Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@rulglj.leidenuniv.nl Tel: [+31] (0)71-274505 ============================================================================= From: IN%"sopekmir@mitr.p.lod.edu.pl" 10-AUG-1994 15:33:20.25 Hello, The HyperCube's HyperChem (info@hyper.com) performs MD simulation using MM+,AMBER,OPLS and BIO+ force fields. it uses cartesian model similar to that used in GROMOS and AMBER. It is very well optimized with respect to speed, and has very good visualizations. However for typical MD calculations it is not easy to calculate some typical data: g(r), vacf etc. I am working on extension which could automaticly calculate these ! We have also implemented GROMOS at our lab on a 486 PC. It works fine, - if you acquire the licence for GROMOS - I could send you our implementation. Now we acquired AMBER and we are working on a PC implementation of this sources! Hope this helps, Mirek dr Miroslaw Sopek Institute of Applied RAdiation Chemistry Technical University Lodz, Poland and: MAKO-lab - HyperCube's dealer in Poland ============================================================================= From: IN%"czarek@sun1.chem.univ.gda.pl" 10-AUG-1994 18:31:02.87 I use Amber 4.0 on PC-486 - it does also Molecular Dynamics calculations. I compile it with NDP Fortran without problems - DOS has no cpp preprocesor and I had to do preprocessing manually but it can be done on Unix to have clear Fortran code and then compile it. With 8 or 16 Mb and 486/66 MHz Amber 4.0 has quite good performance. ============================================================================= From: IN%"hurst@hyper.hyper.com" 10-AUG-1994 19:29:20.12 HyperChem for Windows can do molecular dynamics using one of four force fields or one of eight semi-empirical quantum mechanics methods to calculate the forces on the atoms. It requires at least a 386 with math coprocessor (i.e. not 486SX), 4MB RAM, 20 MB free hard disk space and Windows 3.1. For more information send email to info@hyper.com or download the demo >from www.ccl.net in pub/chemistry/software/MS-WINDOWS/hcdemo.zip. Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ============================================================================= From: IN%"billg@scg.fujitsu.com" 10-AUG-1994 23:14:28.56 Dear Jaime, I would certainly recommend the molecular modeling/computational chemistry software package HyperChem (Hypercube, Inc.) as a possible answer to both of your questions. HyperChem integrates molecular mechanics, molecular dynamics, and semiempirical quantum mechanics together with a graphical user interface and model builder. The MD can be run at constant energy or constant temperature, in vacuo or with solvent, as an isolated cluster or with periodic boundary conditions using either AMBER, Bio+(CHARMM), OPLS, or MM+(MM2) force fields. For Andrew's work, HyperChem offers nine semiempirical Hamiltonians (Extended Huckel, CNDO, INDO, MINDO/3, MNDO, AM1, PM3, ZINDO/1, ZINDO/S). MOPAC and AMPAC also offer semimpirical QM on PC's, and your choice should depend upon your specific problem. For what it's worth, HyperChem was written specifically for PC's. My knowledge of HyperChem is a bit dated, and I'm sure that Graham Hurst (of Hypercube) will respond to these inquiries as well. Hope this helps, Bill ********************************************************************* * William A. Glauser, Ph.D. | Internet: billg@scg.fai.com * * Computational Chemist | Voice: (610) 436-8125 * * SuperComputer Group | FAX: (610) 430-1526 * * Fujitsu America, Inc. | * ********************************************************************* ============================================================================= From: IN%"Keith.Refson@earth.ox.ac.uk" "Keith Refson" 11-AUG-1994 12:12:27.15 Depends on what you mean by "molecular dynamics". This term covers at least two fairly different fields. If you want to model molecules using molecular-mechanics type force fields I can't help. But if you want to do MD simulations of solids or liquids based on small molecules/ions using pair potentials then you may find my MD code "Moldy" of use. Check out the WWW page, URL= http://www.earth.ox.ac.uk/~keith/moldy.html for details. You will need a decent C compiler plus a DOS extender to compile it. Keith Refson ------------------------------------------------------------------------------ | Email : keith@earth.ox.ac.uk | Dr Keith Refson, Dept of Earth Sciences| | TEL(FAX): +44 865 272026 (272072) | Parks Road, Oxford OX1 3PR, UK | ------------------------------------------------------------------------------ From d3f012@pellucidar.pnl.gov Tue Sep 13 15:57:05 1994 Received: from pnlg.pnl.gov for d3f012@pellucidar.pnl.gov by www.ccl.net (8.6.9/930601.1506) id PAA11861; Tue, 13 Sep 1994 15:06:37 -0400 From: Received: from pellucidar.pnl.gov (130.20.182.74) by pnlg.pnl.gov; Tue, 13 Sep 94 11:56 PDT Received: by pellucidar.pnl.gov (920330.SGI/920502.SGI) for @pnlg.pnl.gov:chemistry@ccl.net id AA20380; Tue, 13 Sep 94 11:56:37 -0700 Date: Tue, 13 Sep 94 11:56:37 -0700 Subject: OPLS parameters To: chemistry@ccl.net Message-id: <9409131856.AA20380@pellucidar.pnl.gov> X-Envelope-to: chemistry@ccl.net Are there OPLS parameters for CCl4 ? Mark ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-96 Richland, WA. 99352 The computational chemistry program Argus is available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. ************************************************************************** From steve@carbo.cc.binghamton.edu Tue Sep 13 17:57:07 1994 Received: from carbo.cc.binghamton.edu for steve@carbo.cc.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id RAA13798; Tue, 13 Sep 1994 17:11:11 -0400 Received: by carbo.cc.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA29835; Tue, 13 Sep 94 16:50:29 -0400 Date: Tue, 13 Sep 1994 16:45:19 -0400 (EDT) From: Steven Schafer Subject: Q:Ab Initio programs To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII What ab initio programs are availible as freeware? I know of GAMESS, but are there any others. I am specificly looking with programs that may have a more diverse basis set selection for transition metals. I know that ECP parameters can be inputed into GAMESS, but what about additional basis sets, I don't remember reading anything on this topic. Thanks in advance, Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department Binghamton, New York From news@nntp-server.caltech.edu Tue Sep 13 19:57:10 1994 Received: from piccolo.cco.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.9/930601.1506) id TAA16211; Tue, 13 Sep 1994 19:53:25 -0400 Received: from gap.cco.caltech.edu by piccolo.cco.caltech.edu with ESMTP (8.6.7/DEI:4.41) id QAA18567; Tue, 13 Sep 1994 16:53:17 -0700 Received: by gap.cco.caltech.edu (8.6.7/DEI:4.41) id QAA21551; Tue, 13 Sep 1994 16:53:09 -0700 To: mlist-chemistry@nntp-server.caltech.edu Path: NewsWatcher!user From: pbedwort@juliet.caltech.edu (Pete Bedworth) Newsgroups: mlist.chemistry Subject: Re: CCL:Non-linear optical properties from MOPAC 7 or 93 Followup-To: mlist.chemistry Date: Tue, 13 Sep 1994 16:58:37 -0800 Organization: California Institute of Technology Lines: 18 Message-ID: References: <01HGIQS2EPPI8WW8PU@NPD.UFPE.BR> NNTP-Posting-Host: 131.215.4.119 In article <01HGIQS2EPPI8WW8PU@NPD.UFPE.BR>, <41GLCM@NPD.UFPE.BR> wrote: > Dear Netters, > > I would greatly appreciate receiving references on any paper > which uses non-linear optical properties of organic compounds computed > from MOPAC 7 or 93 using time-dependent formalisms (TDHF or CPHF). > I am aware of the method but I know of no references using it from > semi-empirical calculations. > Thank you, > Gustavo Laureano Coelho de Moura > > 41glcm@npd1.ufpe.br > > > > >Look up the name Jean-Luc Bredas.