From Lommatzsch@chemie.uni-frankfurt.de Thu Apr 17 05:36:49 1997 Received: from anna-atm.rz.uni-frankfurt.de for Lommatzsch@chemie.uni-frankfurt.de by www.ccl.net (8.8.3/950822.1) id EAA18890; Thu, 17 Apr 1997 04:50:46 -0400 (EDT) From: Message-Id: <199704170850.EAA18890@www.ccl.net> Received: from rz.uni-frankfurt.de by anna.rz.uni-frankfurt.de id <21414-0@anna.rz.uni-frankfurt.de>; Thu, 17 Apr 1997 10:50:29 +0000 X-Mailer: exmh version 1.6.1 5/23/95 To: chemistry@www.ccl.net Subject: rotational contour simulation software search Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 17 Apr 97 10:50:28 +0200 X-Host: vulpius.rz.uni-frankfurt.de Sender: Lommatzsch@chemie.uni-frankfurt.de Hello, I am searching for a program, which can be used for a rotational band contour simulation for vibronic transitions for polyatomic molecules (asymmetric- top). Thanks, Uwe Lommatzsch Lommatzsch@chemie.uni-frankfurt.de **************************************************************************** Johann Wolfgang Goethe Universitaet Inst. fuer Physikalische und Theoretische Chemie AK Prof. Dr. Brutschy Marie- Curie- Str. 11 60439 Frankfurt / Main Germany Phone: &49 (69) 798- 29425 Fax: &49 (69) 798- 29560 WWW: http://www.rz.uni-frankfurt.de/~lommatz **************************************************************************** From gerwalin@iris1.chemie.uni-kl.de Thu Apr 17 07:36:52 1997 Received: from uni-kl.de for gerwalin@iris1.chemie.uni-kl.de by www.ccl.net (8.8.3/950822.1) id HAA19712; Thu, 17 Apr 1997 07:35:42 -0400 (EDT) Received: from iris1.chemie.uni-kl.de by news.uni-kl.de id aa25536; 17 Apr 97 13:35 MET DST Received: by iris1.chemie.uni-kl.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id NAA12428; Thu, 17 Apr 1997 13:35:27 +0200 Date: Thu, 17 Apr 1997 13:35:27 +0200 From: Elmar Gerwalin Message-Id: <199704171135.NAA12428@iris1.chemie.uni-kl.de> To: chemistry@www.ccl.net Subject: CCL:Re: drawings (Hi Jeremy) One simple way to save your molecules as an image file is to make a snapshot of your xmol window. You only have to adjust the bonding and atom thickness parameters. To do a snapshot, you may use xv, xwwd(= xwindowdump, both programs are UNIX executables) or any other snapshot program you like. The result is not the very best quality, but may be good enough for most purposes. Bye Elmar ---- Elmar Gerwalin, gerwalin@chemie.uni-kl.de ----- From varnai@bellatrix.pcl.ox.ac.uk Thu Apr 17 07:49:25 1997 Received: from oxmail4.ox.ac.uk for varnai@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA19588; Thu, 17 Apr 1997 07:06:12 -0400 (EDT) Received: from joule.pcl.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Thu, 17 Apr 1997 12:05:48 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.8.5/8.6.5) with SMTP id MAA11945 for <@joule.pcl:chemistry@www.ccl.net>; Thu, 17 Apr 1997 12:05:45 +0100 (BST) Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id MAA25989; Mon, 17 Mar 1997 12:06:03 GMT From: varnai@bellatrix.pcl.ox.ac.uk (Peter Varnai) Message-Id: <199703171206.MAA25989@bellatrix> Subject: gaussian massage To: chemistry@www.ccl.net Date: Mon, 17 Mar 1997 12:05:58 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Dear G9X Users, I would like to ask your help in running a HF/sto-3g massage job. Including the massage keyword and adding the point charge information the program calculates the SCF energy but in the gradient calculation dies with the following error: OPERATION ON FILE OUT OF RANGE. FILEIO: IOPER= 2 IFILNO(1)= 575 LEN= 200000 IPOS= 0 Q= 268680312 dumping /fiocom/, unit = 1 nfiles = 58 sizext = 524288 winblk = 512 defal = T lstwrd = 4349440 ... Error termination in NtrErr: NtrErr called from FileIO. Any help to sort the problem out would be highly appreciated! Peter Varnai From laurent@crypt.u-strasbg.fr Thu Apr 17 09:36:52 1997 Received: from crypt.u-strasbg.fr for laurent@crypt.u-strasbg.fr by www.ccl.net (8.8.3/950822.1) id IAA20338; Thu, 17 Apr 1997 08:46:17 -0400 (EDT) Received: (from laurent@localhost) by crypt.u-strasbg.fr (951211.SGI.8.6.12.PATCH1042/8.6.10) id OAA22125; Thu, 17 Apr 1997 14:46:56 +0200 Date: Thu, 17 Apr 1997 14:46:56 +0200 (MET) From: Laurent TROXLER To: chemistry@www.ccl.net Subject: CCL:Gaussian compilation on a HP PA-8000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Bonjour, Did anyone tried the compilation of Gaussian-94 on an HP 9000/871 computor with a PA-8000 processor under the B.10.20 HP-UX system ? If you succeeded in such achievement, I would be interrested to know the compilation modifications you did in the Makefile and others. Thanks for all, Laurent Troxler ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/\@@/\@@/\@@@@ Laurent TROXLER / \/ \/ \ Lab. Modelisation et Simulations Moleculaires / /\/ /\/ /\ \ Universite Louis Pasteur \ \/ /\/ /\/ / 4, rue Blaise Pascal \ \/\ \/\ \/ 67070 Strasbourg (France) /\ \/\ \/\ \ E-mail: troxler@crypt.u-strasbg.fr / /\/ /\/ /\ \ Tel : (33) 3 88 41 62 87 \ \/ /\/ /\/ / @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\@@/\@@/\@@/@@@ """"""""""""""""""""""""""""""""""""""""""""""""""\/""\/""\/"""" From netsci@awod.com Thu Apr 17 10:36:52 1997 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.8.3/950822.1) id KAA21189; Thu, 17 Apr 1997 10:07:45 -0400 (EDT) Received: from [208.140.96.6] (chs0006.awod.com [208.140.96.6]) by sumter.awod.com (8.7.6/8.6.12) with SMTP id KAA25590; Thu, 17 Apr 1997 10:07:42 -0400 (EDT) X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Apr 1997 10:05:24 +0100 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: April Issue of NetSci The April issue of NetSci is on-line at: http://www.netsci.org This issue includes "World-Wide Web Scientific Publications: Future Potential and Current Problems". From JoelP@agiss.com Thu Apr 17 10:44:56 1997 Received: from seraph.uunet.ca for JoelP@agiss.com by www.ccl.net (8.8.3/950822.1) id JAA20852; Thu, 17 Apr 1997 09:36:57 -0400 (EDT) Received: from agiss by seraph.uunet.ca with UUCP id <656719-18386>; Thu, 17 Apr 1997 09:36:48 -0400 Received: from office.agissa (mailgate) by agiss.com (4.1/SMI-4.1) id AA09327; Thu, 17 Apr 97 09:15:21 EDT Received: by office.agissa with Microsoft Mail id <33564F92@office.agissa>; Thu, 17 Apr 97 09:28:02 PDT From: Joel Polowin To: CCL Every , HChem User Cc: "'94970459@tolka.dcu.ie'" <94970459@tolka.dcu.ie> Subject: RE: HyperChem and Conjugate Gradient Search Methods Date: Thu, 17 Apr 1997 12:18:00 -0400 Message-Id: <33564F92@office.agissa> Encoding: 19 TEXT X-Mailer: Microsoft Mail V3.0 Paddy Kane <94970459@tolka.dcu.ie> writes: > Page 213 of the HyperChem, version 4 manual states that with conjugate > gradient search methods, a descent direction (to lower energy) is chosen > by consdering [among other things - my brackets] the conjugate of the > gradient which is initially the negative of the current gradient. > Could someone please tell me what is meant by the CONJUGATE of a gradient. Take a look in the HyperChem _Computational Chemistry_ manual, in the "Conjugate Gradient Methods" section in the "Computational Options" chapter. All of that stuff is defined/explained there. Joel joelp@agiss.com From joe@mickey.chem.luc.edu Thu Apr 17 11:36:56 1997 Received: from mickey.chem.luc.edu for joe@mickey.chem.luc.edu by www.ccl.net (8.8.3/950822.1) id LAA21817; Thu, 17 Apr 1997 11:14:29 -0400 (EDT) Received: by mickey.chem.luc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA08411; Thu, 17 Apr 1997 10:17:29 -0700 From: joe@mickey.chem.luc.edu (Joseph S Brunzelle) Message-Id: <9704171017.ZM8409@mickey.chem.luc.edu> Date: Thu, 17 Apr 1997 10:17:23 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: md animation for mac Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, does anyone know of a PPC MAC program that will read a charmm trajectory file and do the MD animation? Please respond to joe@mickey.chem.luc.edu Thank You -- -------------------------------------------------------------------------- Joseph S. Brunzelle Loyola University of Chicago Dept. of Chemistry Chicago, IL 60626 Tel. 773-508-3132 Fax. 773-508-3086 ------------------------------------------------------------------------- From shenderm@U.Arizona.EDU Thu Apr 17 13:37:02 1997 Received: from aruba.u.arizona.edu for shenderm@U.Arizona.EDU by www.ccl.net (8.8.3/950822.1) id NAA23147; Thu, 17 Apr 1997 13:08:56 -0400 (EDT) Received: from localhost (shenderm@localhost) by aruba.u.arizona.edu (8.8.5/8.8.5) with SMTP id KAA52518; Thu, 17 Apr 1997 10:06:09 -0700 Date: Thu, 17 Apr 1997 10:06:08 -0700 (MST) From: Mark D Shenderovich To: patrick kane <94970459@tolka.dcu.ie> cc: HChem User , HChem Supp , CCL Every Subject: Re: CCL:HyperChem and Conjugate Gradient Search Methods In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 16 Apr 1997, patrick kane wrote: > > Hi, > > Page 213 of the HyperChem, version 4 manual states that with conjugate > gradient search methods, a descent direction (to lower energy) is chosen > by consdering [among other things - my brackets] the conjugate of the > gradient which is initially the negative of the current gradient. > > Could someone please tell me what is meant by the CONJUGATE of a gradient. > > THanks in response for your replies. > > Rgds, > Paddy. Dear Paddy, CONJUGATE means that the direction of each iterative step is defined as a linear combination of gradient vectirs in at least two consequtive points of the path, i.e. r(i) = a*g(i) + b*g(i-1) + ... This makes conjugated gradient methods very efficient when a starting point is far from an energy mimimum. But, if you have a choice, use second order algorithms (Fletcher-Powel, Newton-Raphson, etc.) when you are close to a minimum and conjugated gradient becomes too slow. Yours, Mark Shenderovich From soperpd@nylon.es.dupont.com Thu Apr 17 14:36:56 1997 Received: from gatekeeper.es.dupont.com for soperpd@nylon.es.dupont.com by www.ccl.net (8.8.3/950822.1) id OAA23711; Thu, 17 Apr 1997 14:16:04 -0400 (EDT) Received: by gatekeeper.es.dupont.com; id OAA06092; Thu, 17 Apr 1997 14:16:03 -0400 Received: by esds01.es.dupont.com; id AA20882; Thu, 17 Apr 97 14:16:02 -0400 Received: (from soperpd@localhost) by nylon.es.dupont.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id OAA29724; Thu, 17 Apr 1997 14:16:40 -0400 Date: Thu, 17 Apr 1997 14:16:40 -0400 Message-Id: <199704171816.OAA29724@nylon.es.dupont.com> From: Paul Soper To: chemistry@www.ccl.net Subject: CCL: Replies on Batch Substructure Searching Reply-To: soperpd@esvax.dnet.dupont.com Many thanks to all those who replied to my question on software for 2D substructure searching: A colleage of mine is looking for a non-interactive program which will take two 2D structures, compare them, and say whether one is present as a substructure in the other. He wants to do a large number of pair-wise comparisons, so batch operation is a must. He'd obviously prefer that the program be available without cost. Here are the replies: ================================================================= The key in such an application is an efficient algorithm for substructure matching. With such an algorithm available, it is quite trivial to make the job done in a batch mode. You can check the following paper for an efficient substructure perception algorithm, but the source code is, unfortunately, not free. Lingran Chen and Wolfgang Robien: MCSS: A New Algorithm for Perception of Maximal Common Substructures and Its Application to NMR Spectral Studies. 1. The Algorithm, J. Chem. Inf. Comput.Sci., 1992, 32, 501-506. Hope this will help. -Lingran Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. 14600 Catalina Street San Leandro CA 94577 Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM URL: http://www.mdli.com http://syngen2.chem.brandeis.edu/~chen/lingran.html ================================================================= Tripos' Unity will do this, although not at zero cost. Cheers, Dave Dr. David A. Winkler Voice: 61-3-9542-2477 Principal Research Scientist Fax: 61-3-9543-8160 CSIRO Division of Chemicals and Polymers http://www.csiro.au Private Bag 10,Clayton South MDC, http://www.wark.csiro.au Clayton 3169, Australia ================================================================= Can't help you with the "without cost" part, but this is definitely possible with CS ChemFinder for Windows and a smidgen of Visual Basic. I've done it. You should have no problem doing several thousand to several tens of thousands of pairs an hour, depending on how fast a machine you're using. More information about ChemFinder is available from http://www.camsoft.com, or >from me in a pinch. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com ================================================================= ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-2112 ----------------------------------------------------------------- From L.Yee@unsw.edu.au Thu Apr 17 19:36:57 1997 Received: from sam.comms.unsw.EDU.AU for L.Yee@unsw.edu.au by www.ccl.net (8.8.3/950822.1) id TAA25517; Thu, 17 Apr 1997 19:22:08 -0400 (EDT) Received: from superam.ceic.unsw.edu.au ([129.94.144.149]) by sam.comms.unsw.EDU.AU (8.7.5/8.7.5.kenso-central) with SMTP id JAA08224 for ; Fri, 18 Apr 1997 09:22:07 +1000 (EST) Message-Id: <3.0.1.32.19970418092331.006a06fc@pop3.unsw.edu.au> X-Sender: p2121821@pop3.unsw.edu.au X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Fri, 18 Apr 1997 09:23:31 +1000 To: chemistry@www.ccl.net From: Lachlan H Yee Subject: CCL: Request Molecular Display of Z-Matrices Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Theoretical Chemists, I am a 1st Year Postgraduate Student at the Uni of New South Wales, I have embarked upon a Polymer Science based project which involves using Gaussian94. I am looking for some simple software that will take a z-matrix file as input and display the molecule in 3D view (and allow rotation of the molecule to view it from several angles etc.) My Friend uses Molecule on the Macintosh to achieve this, but what is the PC equivalent software? Shareware would be preferable. Many thanks, Lachlan Yee. ____________________________ Lachlan H Yee B.Sc. Postgraduate Student Polymer Science Univesity of NSW Sydney 2052 Australia Ph (02) 9385 5512 Fx (02) 9385 5966 Email: l.yee@unsw.edu.au From ykhan@pbo.kaist.ac.kr Thu Apr 17 22:36:59 1997 Received: from pbo.kaist.ac.kr for ykhan@pbo.kaist.ac.kr by www.ccl.net (8.8.3/950822.1) id WAA25892; Thu, 17 Apr 1997 22:18:53 -0400 (EDT) From: Received: by pbo.kaist.ac.kr (AIX 4.1/UCB 5.64/4.03) id AA20000; Fri, 18 Apr 1997 11:20:43 +1000 Date: Fri, 18 Apr 1997 11:20:43 +1000 Message-Id: <9704180120.AA20000@pbo.kaist.ac.kr> To: chemistry@www.ccl.net Subject: SCRF volume Dear Netters, I am interested in SCRF programming. The SCRF calculations require molecular volume, using Onsager model. Can anybody tell me about an independent program which calculate only molecular volume at ab initio methods such as Hartree-Fock level of theory. Young-Kyu Han Department of Chemistry, KAIST South Korea e-mail : ykhan@pbo.kaist.ac.kr