From berriz@chasma.harvard.edu Wed Apr 9 00:34:57 1997 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.3/950822.1) id AAA16081; Wed, 9 Apr 1997 00:24:35 -0400 (EDT) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA20625; Wed, 9 Apr 1997 00:23:11 -0400 Date: Wed, 9 Apr 1997 00:23:11 -0400 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9704090423.AA20625@chasma.harvard.edu> To: chemistry@www.ccl.net In-Reply-To: (ROBMARJ@msn.com) Subject: Molecular modeling kits (Was: dreiding models) From: "ROBERT NICHOLSON" Sender: Computational Chemistry List ANYBODY OUT THERE KNOW OF UK OR USA SUPPLIERS OR EUROPEAN SUPPLIERS OF DREIDING MODELS Now that I have been enlightened about Dreiding models, thanks to helpful CCL readers, I'll use Robert Nicholson's query as point of departure for my own. (I have hesitated to ask until now, on the grounds that the topic is not cutting-edge, high-tech computer stuff, but old-fashioned, low-tech physical models, but, I suppose there are others like me, for whom Quanta, Rasmol, Xmol, &c., are not quite enough). I have been looking for a while for molecular building kits (like Dreiding models) but specialized for polypeptide chains. Any suggestions? In his comprehensive book on proteins, Creighton recommends the so-called "Nicholson components" (any relation to Robert Nicholson? :-) ) as particularly good for modeling proteins, and gives a supplier (Labquip, in the UK). I have contacted Labquip, but so far they have not confirmed whether they still sell these models (I think we can at least say that they are not the hottest selling item among their offerings). Thanks in advance for your suggestions. Gabriel Berriz berriz@chasma.harvard.edu Dept. of Chemistry and Chemical Biology Harvard University 12 Oxford St, Cambridge, MA 02138 USA From genghis@darkwing.uoregon.edu Wed Apr 9 00:54:59 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id AAA16051; Wed, 9 Apr 1997 00:09:23 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.5/8.8.5) with SMTP id VAA09176 for ; Tue, 8 Apr 1997 21:09:21 -0700 (PDT) Date: Tue, 8 Apr 1997 21:09:21 -0700 (PDT) From: Dale Andrew Braden Reply-To: Dale Andrew Braden To: cclpost Subject: geometry optimization methods (more!) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I have been very pleased with the many responses to my question about whether there is any situation in which a Cartesian optimization would be faster than an optimization in redundant internal coordinates. There seems to be a difference of opinion on this, and I hope to keep the discussion going by giving here a summary (in my own words) of the responses so far, as well as a bit more information about my particular problem. I'll give a complete summary later, including due acknowledgment to the many people who have responded. It appears that a cartesian optimization can be faster overall for very large systems, because the overall scaling with cartesians becomes more favorable. I note here that, although the idea of using redundant internal coordinates has been around for some time, not all electronic structure packages employ it. For example, the Spartan program uses Cartesian coordinates. This makes sense if the above is true, since people often use the program to model very large molecules. It also appears that ordinary Z-matrix coordinates are not always inferior to cartesians OR to redundant internals. I was given the example of azulene, whose geometry fails to converge when a redundant internal optimization is performed, but which converges nicely when the optimization is constrained to nonredundant internals. And if the initial geometry is bad, then, even with a good Hessian, a straight Z-matrix optimization can be faster than one in cartesians. I believe I have read somewhere about fused ring systems causing problems for redundant internal coordinates. I have been trying to optimize the structure of a hydrogen-bonded dimer in a solvent medium (which, I neglected to mention, I am treating as a dielectric continuum, and not as a collection of discrete molecules). I first performed the optimization in the absence of a dielectric, so that I would have a good starting geometry and Hessian. In the presence of a dielectric, the geometry failed to converge when I used a straight Z-matrix, even after 30 steps. I then switched to redundant internals (which I should have been using from the start anyway), and it proceeded 3 more steps, and then stumbled into a region in which the energy, forces and displacements went way up. Then the SCF failed, and that was that. The high dielectric medium is causing the problem, since the optimization without it converged rapidly (even using a straight Z-matrix). What I should do is freeze the intermolecular coordinates (whose displacements remained large throughout the failed optimization) and optimize everything else, then unfreeze them, and continue. Again, thank you to all those who have responded so far! Yours, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From eslone@patriot.net Wed Apr 9 02:35:01 1997 Received: from jefferson.patriot.net for eslone@patriot.net by www.ccl.net (8.8.3/950822.1) id CAA16430; Wed, 9 Apr 1997 02:19:16 -0400 (EDT) Received: from eric (th-0-19.patriot.net [206.151.9.28]) by jefferson.patriot.net (8.7.4/8.7.3) with SMTP id CAA32726 for ; Wed, 9 Apr 1997 02:17:37 -0400 Message-ID: <334B350A.549D@patriot.net> Date: Wed, 09 Apr 1997 02:19:54 -0400 From: "J. Eric Slone" Reply-To: eslone@patriot.net Organization: Scientific Consulting Services X-Mailer: Mozilla 3.0Gold (Win95; U) MIME-Version: 1.0 To: Computational Chemistry List Subject: Gaussian TS Problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I'm hoping someone can shed some light on a problem we are experiencing. In determining a transition state of the replacement reaction of the F in sarin (CH3P(=O)(F)OC(CH3)2) with a hydroxyl, we have obtained different results on two different computers. One computer comfirms the transition state with a single imaginary frequency, the other calculates three imaginary frequencies. The calculated energies are also different. The same input is used on both computers. Any ideas? Thanks, Eric ___________________________________________________________________ J. Eric Slone Scientific Consulting Services 5500 Holmes Run Parkway, Suite 501 Alexandria, Virginia 22304-2851 Phone: (703) 461-7078 mailto:eslone@patriot.net Fax: (703) 751-6639 http://www.patriot.net/users/eslone ___________________________________________________________________ "Nature uses only the longest threads to weave her patterns, so each small piece of her fabric reveals the organization of the entire tapestry." Richard P. Feynman From rich@teamscience.com Wed Apr 9 03:35:00 1997 Received: from venus.star.net for rich@teamscience.com by www.ccl.net (8.8.3/950822.1) id CAA16749; Wed, 9 Apr 1997 02:44:12 -0400 (EDT) Received: from lysa (lysa.teamscience.com [199.232.114.18]) by venus.star.net (8.8.5/8.7.3) with SMTP id BAA24256; Wed, 9 Apr 1997 01:38:28 -0500 Message-Id: <3.0.32.19970409025856.009b4960@star.net> X-Sender: richlysa@star.net X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 09 Apr 1997 03:04:31 -0400 To: rich@teamscience.com From: "Rich Lysakowski, Ph.D." Subject: Call for Papers - ACS Symposium on "Electronic Notebooks, Collaborative Computing and Internets/Intranets in Science" - the deadline is approaching Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleague, The 7th International Symposium on "Electronic Notebooks, Collaborative Computing and Internets/Intranets in Science" will be at the ACS Meeting in Las Vegas. THE DEADLINE IS APPROACHING FAST (APRIL 15TH - One week away!!) A few days extension may be possible. If you are doing interesting things with electronic notebooks, groupware, document management, the world wide web or Intranets, or collaborative computing, or LIMS in R&D and scientific applications that you would like to share with other scientists, information specialists, or other professionals working in lab automation, chemical or bioinformatics, intellectual property protection, or related fields... PLEASE SUBMIT A PAPER! ATTACHED IS THE ABSTRACT FORM! [UUENCODED MS-Word for Windows V6.0 template] GENERAL INFORMATION - About the 214th ACS National Meeting The 214th ACS national meeting in Las Vegas will be held September 7-11. The program will appear on this site in addition to the June 2 and August 4, 1997 issues of Chemical and Engineering News. Information on the Las Vegas meeting will be posted as it becomes available. American Chemical Society Meetings Department 1155 Sixteenth Street, N.W. Washington, D.C. 20036 USA Phone: (202) 872-4396 Fax: (202) 872-6128 IF YOU WANT TO PRESENT A PAPER AT THE SYMPOSIUM Download the abstract form either from the ACS website at: http://www.acs.org/meetings/abstract/absdown.html See this next ACS Web link if you don't know how to fill out one of these forms. http://www.acs.org/meetings/abstract/abinfo.html#howto DEADLINE FOR ABSTRACTS The deadline for abstracts is April 15th. PLEASE SEND COPIES OF YOUR ABSTRACT AS A FILE ATTACHMENT TO: Rich Lysakowski at "rich@teamscience.com" [Symposium Chairman] Charlie Gragg at "cgragg@nc.ndl.net" [ACS CINF Division Chairman] HISTORY OF THE SYMPOSIUM SERIES In 1992 Steve Schmidt and Rich Lysakowski committed to host a series of symposia at various international venues to catalyze the creation and acceptance of electronic notebooks and related systems in science. We decided a dozen symposia held over a ten-year period would suffice to "make it happen." We've had six symposia so far and we are most of the way there now. From csonka@lctn.u-nancy.fr Wed Apr 9 04:35:00 1997 Received: from host11.lctn.u-nancy.fr for csonka@lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id EAA17072; Wed, 9 Apr 1997 04:30:41 -0400 (EDT) Received: from host12.lctn.u-nancy.fr (pc4 [192.54.210.106]) by host11.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) with ESMTP id KAA30090; Wed, 9 Apr 1997 10:31:05 +0200 (DFT) Message-ID: <334B45AE.392F@lctn.u-nancy.fr> Date: Wed, 09 Apr 1997 09:30:54 +0200 From: Csonka Gabor Organization: Laboratiore de Chimie Theorique, Nancy X-Mailer: Mozilla 4.0b2 (Win95; I) MIME-Version: 1.0 To: "E. Lewars" Subject: Re: CCL:PM3 AND AM1 FOR H BONDS X-Priority: 3 (Normal) References: <199704081630.MAA12779@alchemy.chem.utoronto.ca> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii E. Lewars wrote: 1997 April 8 There was a recent question about AM1 vs. PM3 for studying hydrogen bonds. Dr J. J. P. Stewart, the inventor of PM3, tells me that he can't find a specific ref to this, but Shields has published on the superiority of PM3 in the last 3 years or so. Some other refs to PM3 cf. AM1 (I don't know offhand if any of these are on H bonding): If you try to optimize the water dimer with PM3, you get the right geom.; if you use AM1 you get the wrong one. See too "Experiments in Computational Organic Chemistry", by Hehre, Burke, Shusterman and Pietro (Wavefunction, 1993), p. 43, where PM3 is recommended for H-bonded molecules because, it is said, it works better than AM1. E. Lewars Chem Dept Trent U, Peterborough Ontario Canada I noticed Dr J. J. P. Stewart via E-mail about the problems with PM3, and we are publishing a paper on this problem. The paper was accepted for THEOCHEM and I'll present the problem on the next ICQC too. In short: the equilibrium geometry is sometimes good, but the hypersurface is wrong. The error is in the oscillating nature of the Gaussian correction functions of the CRF in PM3. This is why the PM3 fails seriously for sugars, c.f. G.I. Csonka, K. Elias, I.G. Csizmadia, J. Comp. Chem., 18 (1997) 330-342 and references therein. See more details and references in: http://web.inc.bme.hu/~csonka/crf/crf.htm Gabor I. Csonka e-mail: csonka@web.inc.bme.hu Lab.Chimie Theorique Universite Henri Poincare B.P. 239 54506 Vandoeuvre-les-Nancy FRANCE tel: +33-3.83.91.25.29 fax: +33-3.83.91.25.30 http://www.ch.bme.hu/inc/csg.html From stephen_andruski@fmc.com Wed Apr 9 09:35:02 1997 Received: from igw.fmc.com for stephen_andruski@fmc.com by www.ccl.net (8.8.3/950822.1) id JAA17978; Wed, 9 Apr 1997 09:01:03 -0400 (EDT) Received: by igw.fmc.com id AA05436 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 9 Apr 1997 08:01:03 -0500 Message-Id: <199704091301.AA05436@igw.fmc.com> Received: by igw.fmc.com (Internal Mail Agent-1); Wed, 9 Apr 1997 08:01:03 -0500 Mime-Version: 1.0 Date: Wed, 9 Apr 1997 08:41:53 -0500 From: stephen_andruski@fmc.com (STEPHEN ANDRUSKI) Subject: Re:drawings To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part There are lots of programs out there if you look around, but finding something that makes nice vector images is difficult. The commercial program "Nemesis" from Oxford Molecular will give Windows Meta Files (WMF) directly off the Windows clipboard. I don't know if it runs under NT though. PCModel for Windows will produce ORTEP or PLUTO drawings and save them as HPGL files, but I've found the implementation buggy. Your best bet is probably ORTEP-III. I believe that there is a Windows NT version available through the ORTEP-III site at: http://www.ornl.gov/ortep/ortep.html There is also a somewhat better GUI implementation "ORTEP-III for Windows" at: http://www.chem.gla.ac.uk/~louis/ortep3/ I run this under Windows 95 but I haven't tried it under NT. With ORTEP you will be able to produce HPGL files and using the appropriate software, convert them into any other vector format or use them directly. ORTEP-III for Windows will read in XYZ files directly. You can change ellipse types and bond types individually or globally and get very nice drawings this way. Hope this helps. I'd be interested in any other programs that you find. Dr. Stephen W. Andruski FMC Corporation stephen_andruski@fmc.com From ludek@ics.muni.cz Wed Apr 9 12:35:05 1997 Received: from elessar.ics.muni.cz for ludek@ics.muni.cz by www.ccl.net (8.8.3/950822.1) id LAA19366; Wed, 9 Apr 1997 11:51:54 -0400 (EDT) Received: from dior.ics.muni.cz (dior.ics.muni.cz [147.251.6.10]) by elessar.ics.muni.cz (8.8.5/8.8.5) with ESMTP id RAA02619 for ; Wed, 9 Apr 1997 17:51:29 +0200 (MET DST) Received: from narya.ics.muni.cz (ludek@narya.ics.muni.cz [147.251.3.16]) by dior.ics.muni.cz (8.8.5/8.8.5) with ESMTP id RAA29522 for ; Wed, 9 Apr 1997 17:51:33 +0200 (MEST) Received: (from ludek@localhost) by narya.ics.muni.cz (8.8.5/8.6.9) id RAA27745 for chemistry@www.ccl.net; Wed, 9 Apr 1997 17:51:31 +0200 (MET DST) From: Ludek Matyska Message-Id: <199704091551.RAA27745@narya.ics.muni.cz> Subject: G94 basis set problem To: chemistry@www.ccl.net Date: Wed, 9 Apr 1997 17:51:31 +0200 (MET DST) X-Mailer: ELM [version 2.4ME+ PL25 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL, I got the following problem when using Gaussian 94 (rev. D.4). Doing some calculations with an in house defined basis set (for Hg) I got the following message (after one and half hour of CPU on our R10000 based POWER Challenge): **** Fatal Problem: The largest alpha MO coeffient is 0.11335235D+04 Error termination via Lnk1e in /packages/run/g94_D4/g94/l801.exe. The calculation was single point SCF MP2=Full. As the guess is that there is some problem with the check on linear dependency of the defined basis, I would like to ask you for any option/parametr how to reduce the internal cutoff values for this case. Any help will be really appreciated. Thank you very much in advance. Ludek Matyska, PhD Institute of Computer Science Masaryk University Botanicka 68a 602 00 Brno Fax: ++420-5-41212747 Czech Republic Phone: ++420-5-41512213 e-mail: ludek@ics.muni.cz ++420-5-740267 From rachelle@picard.niehs.nih.gov Wed Apr 9 13:35:06 1997 Received: from picard.niehs.nih.gov for rachelle@picard.niehs.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA19783; Wed, 9 Apr 1997 12:43:40 -0400 (EDT) Received: from picard (localhost [127.0.0.1]) by picard.niehs.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA00570 for ; Wed, 9 Apr 1997 12:47:58 -0400 Sender: rachelle@picard.niehs.nih.gov Message-ID: <334BC83E.41C6@picard.niehs.nih.gov> Date: Wed, 09 Apr 1997 12:47:58 -0400 From: "Rachelle J. Bienstock" X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX64 6.2 IP26) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Molscript Makefile compilation problem... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi- Since I upgraded my SGI to Irix 6.2, I have been recompiling all my old COFF exectuables (since 6.2 no longer supports COFF binaries). I am now trying to recompile Molscript and have encountered the following error... (the compilation begins correctly...creating the object files- f77 -c -O1 -u molscript.f f77 -c -O1 -u schematic.f f77 -c -O1 -u graphics.f f77 -c -O1 -u ps.f But then it says... don't know how to make ../forlib/forlib.a (bu42). Can anyone explain or assist with this problem? Thanks, rachelle From elewars@alchemy.chem.utoronto.ca Wed Apr 9 16:35:09 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id PAA20999; Wed, 9 Apr 1997 15:51:11 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id PAA28097 for chemistry@www.ccl.net; Wed, 9 Apr 1997 15:51:10 -0400 (EDT) Date: Wed, 9 Apr 1997 15:51:10 -0400 (EDT) From: "E. Lewars" Message-Id: <199704091951.PAA28097@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: DRAWING PROGRAM 1996 June 26 Hello, This is in response to a question about a program that will accept molecular geometry in various formats (e.g. XYZ, Gaussian) and give nice pictures (a drawing program). The Windows program Molwin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. MolWin will also accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. E. Lewars ==== From 94970459@tolka.dcu.ie Wed Apr 9 18:35:09 1997 Received: from tolka.dcu.ie for 94970459@tolka.dcu.ie by www.ccl.net (8.8.3/950822.1) id SAA21955; Wed, 9 Apr 1997 18:05:12 -0400 (EDT) Received: by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA15000; Wed, 9 Apr 1997 23:04:10 +0100 Date: Wed, 9 Apr 1997 23:04:10 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: CCL Every , HChem User , HChem Supp Subject: Dihedral Angle Driver and HyperChem Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I read that the MM2 force field contains a DIHEDRAL ANGLE DRIVER, which allows the user to scan part of the potential surface in search of local minima. Can anyone tell me if the MM+ force field which is available in HyperChem (and which is a variation of the MM2 force field) contains this facility? If so, how does it compare to other conformational search methods such as simulated annealing. Thanks in advance for your replies. Rgds, Paddy. ************************************************************************* * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************* From sxr224@anugpo.anu.edu.au Wed Apr 9 19:35:07 1997 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.8.3/950822.1) id TAA22262; Wed, 9 Apr 1997 19:04:56 -0400 (EDT) Received: from surya.anu.edu.au (surya.anu.edu.au [150.203.193.135]) by anugpo.anu.edu.au (8.8.5/8.8.5) with SMTP id JAA29450; Thu, 10 Apr 1997 09:04:54 +1000 (EST) Message-Id: <199704092304.JAA29450@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba.Ranganathan" To: chemistry@www.ccl.net, "Rachelle J. Bienstock" Date: Thu, 10 Apr 1997 09:03:04 +0000 Subject: Re: CCL:Molscript Makefile compilation problem... Reply-to: Shoba.Ranganathan@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Hi Rachelle, > > (the compilation begins correctly...creating the object files- > f77 -c -O1 -u molscript.f > f77 -c -O1 -u schematic.f > f77 -c -O1 -u graphics.f > f77 -c -O1 -u ps.f try putting in -32: all the "old" programs work without a hitch then. Else, a version compiled at IRIX 5.3 will surely run without any problems: let me know if you want this version. Shoba =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)==============