From laaksone@csc.fi Thu Feb 2 01:41:39 1995 Received: from finsun.csc.fi for laaksone@csc.fi by www.ccl.net (8.6.9/930601.1506) id BAA04340; Thu, 2 Feb 1995 01:26:39 -0500 Received: by finsun.csc.fi id AA06077 (5.65c8+/IDA-1.4.4 for chemistry@ccl.net); Thu, 2 Feb 1995 08:26:33 +0200 Date: Thu, 2 Feb 1995 08:26:33 +0200 (EET) From: Leif Laaksonen Subject: Chemistry on PC:s To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Computational Chemists, Now when I can see that it's fully allowed to discuss about the Web on the CCL list I would like to ask the user community about a problem, which is strictly speaking not chemistry, I have not been able to solve myself. I believe there has always been a sort of ambivalent relation between (graphics)workstations and the PC:s. Workstations used to be Unix machines and the PC:s were DOS/Windows or Macintosh machines. Unix had all the nice networking (TCP/IP) features included so it was also very easy to network them. The graphics workstations again had also very powerful graphics boards so they could be used for demanding display purposes. The drawback for the PC:s (in the beginning) was the lack of standard networking hardware, software and 3D graphics libraries which prevented the PC:s to be taken "seriously" in the computational fields. I just want to remind you about the discussion here in CCL list about the HyperChem program, some time ago. However, things have changed a lot during the last years. Today we have PC operating systems like Windows NT or OS/2 (Warp) which allows us to combine all the PC/Windows programs available today with the networking power TCP/IP gives us. Windows NT even has the SGI 3D graphics library OpenGL which allows us to run (almost) the same applications on a PC today that we used to run on Unix machines yesterday. Soon we will even have special OpenGL graphics boards which allow us to run graphics applications much faster than today. My question is now, is there any demand (need) to write graphics programs for computation chemists for the PC (Windows NT) market? I am talking about client/server programs where the graphics would be sitting on the PC and the computationally intensive parts would be done on other machines. This would give us the possibility to cut and past graphics and data direct to PC applications like word processors or spreadsheets. If everybody already has a Unix graphics workstation in front of them I would not expect the PC business be worth too much (for the computational chemists) but if people still use PC:s regularly there might still be some interest. One further aspect is also the fact that we can also run Windows NT on "real" graphics workstations today. However, I don't know about any computational chemistry applications ported to the graphics workstation/Windows NT platform. Would any of you want to change the Unix on your graphics workstation into Windows NT? If you have any opinions/ideas about these things, please let me know. Thank you very much for your help. Regards, -leif laaksonen Ps. I know about the Linux software for the PC:s but Linux does not so far allow me to run PC/Windows applications. ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- I dreamed that, as I wandered by the way, Bare winter suddenly was changed to spring. P.B. Shelley ------------------------------------------------------------------- From HRUSAK@jh-inst.cas.cz Thu Feb 2 02:41:40 1995 Received: from uivt1.uivt.cas.cz for HRUSAK@jh-inst.cas.cz by www.ccl.net (8.6.9/930601.1506) id CAA04830; Thu, 2 Feb 1995 02:02:12 -0500 Received: from bob223.jh-inst.cas.cz ([147.231.28.65]) by uivt1.uivt.cas.cz (4.0/SONY-4.0MX) id AA08636; Thu, 2 Feb 95 08:00:24 +0100 Received: from BOB/MAILQUEUE by bob223.jh-inst.cas.cz (Mercury 1.20); 2 Feb 95 08:00:57 GMT+1 Received: from MAILQUEUE by BOB (Mercury 1.20); 2 Feb 95 08:00:39 GMT+1 From: "Dr. Jan Hrusak" Organization: Institute of Physical Chemistry To: chemistry@ccl.net Date: Thu, 2 Feb 1995 08:00:37 +0100 Subject: DFT anions ? Return-Receipt-To: "Dr. Jan Hrusak" Priority: normal X-Mailer: Pegasus Mail/Windows (v1.22) Message-Id: <2864F1007A@bob223.jh-inst.cas.cz> Dear Neters, could somebody in the list point me to a reference for DFT applicaions to molecular anions. Jan Hrusak ---------------------------------------------------------------------------- Dr. Jan Hrusak ############################### J. Heyrovsky Institute of Physical Chemistry ## MEMOR ESTO CONGREGATIONIS ## Academy of Sciences of the Czech Republic ## TVAE QVAM POSSEDISTI ## Dolejskova 3, CZ-182 23 Prague 8 ## AB INITIO ## Czech Republic ############################### ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Phone: (0042 2) 66 05 3436 FAX: (0042 2) 858 2307 E-Mail: hrusak@jh-inst.cas.cz ---------------------------------------------------------------------------- From gbaudoux@quick.cc.fundp.ac.be Thu Feb 2 05:41:49 1995 Received: from hermes.fundp.ac.be for gbaudoux@quick.cc.fundp.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA06816; Thu, 2 Feb 1995 05:35:35 -0500 From: Received: by hermes.fundp.ac.be; id AA26735; Thu, 2 Feb 1995 11:41:31 +0100 Received: from quick.cc.fundp.ac.be by hermes.fundp.ac.be; id AA26735; Thu, 2 Feb 1995 11:41:31 +0100 Date: Thu, 2 Feb 1995 11:26:52 +0200 Message-Id: <95020211265229@quick.cc.fundp.ac.be> To: chemistry@ccl.net Subject: searching for Threader X-Vms-To: SMTP%"chemistry@ccl.net" Hello! I am searching for the program Threader of D.Jones. It is a program for fold recognition from protein sequences. Please send any information to my email address. Thanks in advance, Guy Baudoux University of Namur Rue de Bruxelles, 61 5000 Namur, Belgium email: gbaudoux@quick.cc.fundp.ac.be From mmccar@postman.essex.ac.uk Thu Feb 2 06:41:45 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA07362; Thu, 2 Feb 1995 05:58:41 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <27860-0@postman.essex.ac.uk>; Thu, 2 Feb 1995 10:58:02 +0000 From: Mccarron M Date: Thu, 2 Feb 95 10:57:54 GMT Message-Id: <12952.9502021057@solb1.essex.ac.uk> To: chemistry Subject: CHARMM Could anybody out there tell me if it is possible to solvate using CHARMM. I know that CHARMM can recognise molecules already solvated but is it possible to solvate with this program like you can with AMBER say. Thanks for you help mail mmccar@essex.ac.uk From thuber@Physik.TU-Muenchen.DE Thu Feb 2 08:41:45 1995 Received: from srv.cip.physik.tu-muenchen.de for thuber@Physik.TU-Muenchen.DE by www.ccl.net (8.6.9/930601.1506) id IAA08381; Thu, 2 Feb 1995 08:08:46 -0500 Received: from speedy.cip.physik.tu-muenchen.de by srv.cip.physik.tu-muenchen.de with SMTP id AA01360 for (5.67a/IDA-1.5/bs04); Thu, 2 Feb 1995 14:07:19 +0100 Received: by speedy.cip.physik.tu-muenchen.de (4.1/SMI-4.1) id AA25541; Thu, 2 Feb 95 14:07:19 +0100 Date: Thu, 2 Feb 95 14:07:19 +0100 From: Thomas.Huber@Physik.TU-Muenchen.DE Message-Id: <9502021307.AA25541@speedy.cip.physik.tu-muenchen.de> To: CHEMISTRY@ccl.net Subject: Summary: van der Waals parameters from ab initio calc 10 days ago I submitted the following question to CCL, the answers I got are appeded: Subject: van der Waals parameters from ab initio calc? Hi netters! Could you please tell me how to derive van der Waals parameters from ab initio calculations! Any suggestions are wellcome (references, principles,...). I'm interested in practical as well as theoretical approaches to this problem. If I got interesting response, I'll collect them and post it to this group! Thank you for help! Thomas Thomas Huber Institut fuer Physikalische Biochemie der Universitaet Muenchen Schillerstrasse 44 80336 Muenchen Germany email: thuber@physik.tu-muenchen.de Return-Path: YQIN@aardvark.ucs.uoknor.edu Dear Huber: Thank you for posting such interesting question. Eventhough I can not give you answer, but I would like to see the summary if you can get enough. Thank you very much in advarce With my best regards yuli qin yqin@aardvark.ucs.uoknor.edu From: jxh@ibm12.biosym.com (Joerg Hill) Hi, sorry for wasting bandwidth, but a direct response did not work. Van-der-Waals parameters for repulsion can be obtained from ab initio calculations using a test particle ansatz. The most papers have been published by Ahlrichs: H.-J. Boehm, R. Ahlrichs: JCP 77 (1982) 2028 H.-J. Boehm, R. Ahlrichs, P. Scharf, H. Schiffer: JCP 81 (1984) 1389 are the both basic paper. Applications can be found in: H.-J. Boehm, C. Meissner, R. Ahlrichs: Mol. Phys. 53 (1984) 651 K. P. Sagarik, R. Ahlrichs, S. Brode: Mol. Phys. 57 (1986) 1247 K. P. Sagarik, R. Ahlrichs: Chem. Phys. Letters 131 (1986) 74 K. P. Sagarik, R. Ahlrichs: JCP 86 (1987) 5117 J.-R. Hill, J. Sauer: JPC 98 (1994) 1238 A new paper, which considers anisotropy is: A. J. Stone, C.-S. Tong: JCC 15 (1994) 1377 I don't know any papers concerning the derivation of dispersive parameters from ab initio calculations. But dispersion requires electron correlation and since these calculations are rather expensive, it could be that noone has triesd it so far. Density Functional calculations could change this. Tschuess Joerg P.S.: host name Physik.TU-Muenchen.DE NOT FOUND. -------------------------------------------------------------------------------- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym Technologies, Inc. | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte, 1830 -------------------------------------------------------------------------------- The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products send mail to: rcenter@biosym.com. -------------------------------------------------------------------------------- Return-Path: helden@gaucho.ucsb.edu Servus, We are interested in the ineraction of helium with small to medium small (10 - 200 atoms) molecules. We found that with the MM3 vdW parameters (Theochem, 312 (1994) 69), we can reproduce our experimental results (gas phase mobilities) very well. I also tried to calculate vdW parameters for He-He and H3C-H - He. In order to get the attractive part of the potential right, one has to throw in a lot of correlation (CCSD(t)) and large basis sets (tripple zeta+pol.+diffuse). The repulsive part of the potential on the other hand is well described by plain SCF + small basis set. I did a scan of the pot. surface of H3C-H - He and found that fitting a 12-6 potential to the scan gives very poor agreement while an exp.-6 potential is much better. The well depth and the position for these two systems seems to be in reasonable good agreement with the MM3 parameters. Contact me if you want to know more about what we are doing, ....Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Return-Path: states@ibc.wustl.edu |> Thomas Huber wrote: |> Could you please tell me how to derive van der Waals parameters from |> ab initio calculations! |> Any suggestions are wellcome (references, principles,...). For condensed matter, there is a fundamental problem with the derivation of non-bonded interactions from ab initio calculations on isolated molecules. High quality ab initio calculations include wavefunctions with quite large spatial extents, much larger than existence in a condensed matter environment would allow. So, if you are going to calculate non-bonded interactions, you need to start with realistic calculations including multiple molecules. The energy of interaction is straightforward. Deciding how much of it is "van der Waals" is another issue. David States From: underhil@hp.rmc.ca (Ross Underhill) Subject: Re: CCL:van der Waals parameters from ab initio calc? >Could you please tell me how to derive van der Waals parameters from ab initio >calculations! >Any suggestions are wellcome (references, principles,...). >I'm interested in practical as well as theoretical approaches to this problem. >If I got interesting response, I'll collect them and post it to this group! A very interesting question and one I have tried to deal with myself. For some elements you can put together two diatomics and bring them together using ab initio calcs and plot the total energy. You can then fit the calculated energy as a function of separation. I have done this in a few cases. I've even done it for methane. You really should do it using UHF since a lot of the attraction at long distances has to do with correlation energy. Obviously this scheme will not work for some elements that don't make diatomics or small simple molecules. There is also the point that this only seems to make sense for closed shell systems. It seems to me I saw some references on deriving VDW parameters on the AMBER WWW site. You might want to look there. I picked up some F parameters there. Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 Return-Path: mizan@engin.umich.edu A possible reference for Nonbonding interactions from ab initio calculations may be: Dinur, U. and A.T. Hagler, J. Am. Chem. Soc., 111, 5149-5151, 1989. Hope this helps. Tahmid Mizan University of Michigan Return-Path: d-white1@assistant.beckman.uiuc.edu Thomas Please either summarize this for the net or send me a copy of the replies. I am really intereted in this myself. Sincerely David White **************************************************************************** * * * * David White * Man is the best computer we can put * * Postdoctoral Research Associate * aboard a spacecraft -- and the only * * Beckman Institute * one that can be mass produced with * * (217) 244-1733 * unskilled labour * * (217) 244-8371 (fax) * Werner von Braun * * * * **************************************************************************** From dodik@yfaat.ch.huji.ac.il Thu Feb 2 10:41:46 1995 Received: from shum.cc.huji.ac.il for dodik@yfaat.ch.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id JAA09942; Thu, 2 Feb 1995 09:42:11 -0500 Received: from yfaat.ch.huji.ac.il by shum.cc.huji.ac.il with SMTP id AA26862 (5.67bHU/IDA-1.5 for ); Thu, 2 Feb 1995 16:41:43 +0200 Received: by yfaat.ch.huji.ac.il (AIX 3.2/UCB 5.64/4.03) id AA38244; Thu, 2 Feb 1995 16:37:42 +0200 Date: Thu, 2 Feb 1995 16:37:42 +0200 From: dodik@yfaat.ch.huji.ac.il (David Danovich) Message-Id: <9502021437.AA38244@yfaat.ch.huji.ac.il> To: chemistry@ccl.net Subject: CCL: G2+ theory Dear Netters, I was asked to do G2+ theory calculations. I know about G2 theory but not about G2+. Could anyone tell me what is G2+ theory and give me a reference? Thank you in advanve. David +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. David Danovich | Internet: dodik@yfaat.ch.huji.ac.il Computational Chemist | Office phone: (+972)-2-586934 Department of Organic Chemistry | FAX: (+972)-2-585345 The Hebrew University, Givat-Ram Campus, | Home phone: (+972)-2-789544 91904 Jerusalem, Israel | +=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From hs@ccl.net Thu Feb 2 10:54:08 1995 Received: from helix for hs@ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA10651; Thu, 2 Feb 1995 10:06:15 -0500 Received: by helix (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA25628; Thu, 2 Feb 95 16:04:46 +0100 From: "Hellfried Schreiber" Message-Id: <9502021604.ZM25626@helix.mdy.univie.ac.at> Date: Thu, 2 Feb 1995 16:04:44 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Conference Announcement Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 >> INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY << Organized by the Austrian Chemical Society Vienna (Austria), September 17-20, 1995 TOPICS: 1) The Impact of Molecular Biology on Structural Biology 2) Biomolecular Structure Determination a) X-Ray Diffraction b) NMR Spectroscopy 3) Dynamics and Function of Biomolecules 4) Computational Methods 5) Protein Engineering and Design Speakers include: Tom Blundell(UK), Hans-J. Boehm(D), Charles Cantor(USA), Christopher Dobson(UK), Manfred Eigen(D), Alan Fersht(UK), Robert Huber(D), Oleg Jardetzky(USA), Martin Karplus(USA), Joseph Lakowicz(USA), Paul Roesch(D), Ilme Schlichting(D), Jeffrey Skolnick(USA), Malcom Walkinshaw(CH) Posters are invited on any of the conference topics Outstanding posters will be selected for 20 minute oral presentations Abstract deadline: MAY 31, 1995 Head of Scientific Committee: P.Schuster Preliminary Participation Fees: Regular Participant 4000 ATS GOeCH Member 3500 ATS Student 2000 ATS For further information and preregistration, contact: A.Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: (43) 1 587249 FAX.: (43) 1 587966 e-mail: msb95@helix.mdy.univie.ac.at -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@helix.mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 4028525 | | | | +-----------------------------------------------------------------------------+ From roger@proteus.co.uk Thu Feb 2 12:41:48 1995 Received: from eros.britain.eu.net for roger@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id MAA13959; Thu, 2 Feb 1995 12:04:35 -0500 Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Thu, 2 Feb 1995 12:24:19 +0000 From: Roger Mee Message-Id: <9502021130.ZM27949@Inca.proteus.co.uk> Date: Thu, 2 Feb 1995 11:30:46 +0000 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: High resolution molecular graphics Cc: r.a.sykes@proteus.co.uk Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hello, I am enquiring to see whether anyone out there has written or is aware of an interface between the Ribbons package of Mike Carson and Raster3D the high resolution image rendering package distributed by Ethan Merritt. I am aware that the Molscript package is closely linked to Raster3D, but I would be interested to see if the alternative route is possible. Alternatively if anyone can suggest other solutions to the problem of creating high resolution (up to 400dpi) molecular graphics images on SGI platforms then please let me know. Please mail me direct and I will summarise to the list. Thanks Roger -- ---------------------------------------------------------------- Roger Mee | tel +44 (0) 625-500 555 | Proteus Molecular Design | fax +44 (0) 625-500 666 | Lyme Green Business Park | roger@proteus.co.uk | Macclesfield, UK. SK11 0JL | | ---------------------------------------------------------------- From hcj@mazda.wavefun.com Thu Feb 2 12:54:29 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.9/930601.1506) id MAA14336; Thu, 2 Feb 1995 12:23:22 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA08118; Thu, 2 Feb 95 09:23:24 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA22433; Thu, 2 Feb 95 09:23:22 -0800 Date: Thu, 2 Feb 95 09:23:22 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9502021723.AA22433@mazda.wavefun.com> To: laaksone@csc.fi Cc: chemistry@ccl.net In-Reply-To: (message from Leif Laaksonen on Thu, 2 Feb 1995 08:26:33 +0200 (EET)) Subject: Re: CCL:Chemistry on PC:s Reply-To: hcj@wavefun.com >>>>> "Leif" == Leif Laaksonen writes: Leif> My question is now, is there any demand (need) to write Leif> graphics programs for computation chemists for the PC Leif> (Windows NT) market? I am talking about client/server Leif> programs where the graphics would be sitting on the PC and Leif> the computationally intensive parts would be done on other Leif> machines. This would give us the possibility to cut and Leif> past graphics and data direct to PC applications like word Leif> processors or spreadsheets. If everybody already has a Unix One solution that is present already is when using modelling programs that support X-windows, such as Spartan (obligatory plug 8^), the graphics can actually be displayed on your PC or Mac while the program runs on a workstation. This is done by running an X-windows server on the PC or Mac, of which there are several available, and telling the client, the modelling program, to which display server it should connect. This will in most cases allow the cut and paste capabilities as well. Here at Wavefunction we have tested our graphics with MacX, for the Mac or course, and PC-Xware for Windows 3.1. They both work quite well. -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From oesterei@hrz.ba-freiberg.de Thu Feb 2 14:42:05 1995 Received: from orion.hrz.ba-freiberg.de for oesterei@hrz.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id OAA16787; Thu, 2 Feb 1995 14:24:58 -0500 Message-Id: <199502021924.OAA16787@www.ccl.net> Received: by orion.hrz.ba-freiberg.de (1.38.193.5/15.6) id AA00747; Thu, 2 Feb 1995 20:24:03 +0100 From: Ralf Oestereich Subject: How to handle "COLLAGE" saved HDF files? To: chemistry@ccl.net (Computer Chemistry List) Date: Thu, 2 Feb 95 20:24:01 MEZ Mailer: Elm [revision: 70.85.2.1] Dear netters. We have to following problem: To make some hardcopies of SPARTAN images, we just tried to grap the screen with COLLAGE. Now the question for us is, how can we convert these HDF-format files, into a printable postscript version? Thats the problem so far! Thank you very much for your attention and your help! Sincerly, R. Oestereich Insitut f. Anorganische Chemie Leipziger Strasse 09599 Freiberg GERMANY From michael@bch48.bch.ncsu.edu Thu Feb 2 15:01:07 1995 Received: from bch48.bch.ncsu.edu for michael@bch48.bch.ncsu.edu by www.ccl.net (8.6.9/930601.1506) id OAA17013; Thu, 2 Feb 1995 14:29:16 -0500 Received: by bch48.bch.ncsu.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA27849; Thu, 2 Feb 95 14:29:06 -0500 From: "Michael R Rothwell" Message-Id: <9502021428.ZM27847@bch48.bch.ncsu.edu> Date: Thu, 2 Feb 1995 14:28:56 -0500 In-Reply-To: Leif Laaksonen "CCL:Chemistry on PC:s" (Feb 2, 8:26am) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Leif Laaksonen , chemistry@ccl.net Subject: Re: CCL:Chemistry on PC:s Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 You can even compile (supposedly) X11.R6 onto an NT machine. For regular old windows, Hummingbird software makes a package called "eXceed/W" that is an X11.R5 server (or is that client?) and lets you have your Unix machine send its display to the PC. You can copy text back and forth. Combined with a program like PC-NFS or just an ftp server for windows (like Novell's), a PC makes a great front end for Unix workstations. Here at NCSU many people do not have their own Unix machines, but need to use Unix power & software; we use eXeec to xlogin to one of several compute servers on campus. A co-worker of mine does his SAS work on a faraway SparcStation from the PC but edits the input & output in Microsoft Word, all without leaving the PC. I used to use a PC as the display for one very old SparcStation, because it was actually -faster-, and I got a lot of colors and use of the PC's graphic accelerator. eXceed won't support OpenGL, but you can buy translator programs which convert OpenGL graphics into standard X. Is this the sort of thing you're talking about? From fox@fenris.ucsf.EDU Thu Feb 2 15:41:52 1995 Received: from cgl.ucsf.EDU for fox@fenris.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id PAA17996; Thu, 2 Feb 1995 15:13:08 -0500 Received: from fenris.ucsf.EDU (fenris.ucsf.EDU [128.218.14.26]) by cgl.ucsf.EDU (8.6.7/GSC4.24) with SMTP id MAA26679 for ; Thu, 2 Feb 1995 12:13:05 -0800 Received: by fenris.ucsf.EDU (1.38.193.4/GSC4.21) id AA16001; Thu, 2 Feb 1995 12:13:03 -0800 From: fox@fenris.ucsf.EDU (Thomas Fox) Message-Id: <9502022013.AA16001@fenris.ucsf.EDU> Subject: G92-DFT bug? H and LYP To: CHEMISTRY@ccl.net Date: Thu, 2 Feb 95 12:13:03 "PST Mailer: Elm [revision: 70.85] Dear CCLers, I was using the DFT module of Gaussian 92 (HP-PARisc-HPUX-G92/DFT-RevF.4) and came across something that looks like a bug to me: when I try to calculate an one-electron system (like the H atom) and use the Lee-Yang-Parr functional, my G92 version stops with an IEEE division by zero error. I browsed through the code, and sure enough found in the LYP subroutine a division by Rho(Beta), which is, in the case of one electron, equal zero. I dont have access to the original paper right now, so could someone just reassure me that this behavior is definitely an unexpected one, and that it doesnt mean that the LYP functional is not valid in the limit of one electron or if I only have electrons of one spin species (Gaussian shouldnt abort that ungracefully, anyway...). A related question is how to get in contact with these Gaussian guys...I sent a message to help@gaussian.com some weeks ago, but havent heard from them back. And, could anybody who has access to a DFT implementation (maybe there is even a G92 version out there that doesnt show this behavior) that supports Becke 3 parameter XC in connection with the LYP C functional calculate the energy for a H radical (with a 6-31G* basis) for me? Pointers to papers where this has been done (maybe as a test case for the functional) are, of course, also highly welcome. Thanks a lot, Thomas -- Thomas Fox e-mail: fox@cgl.ucsf.edu Dept. of Pharmaceutical Chemistry University of California San Francisco, CA 94143-0446 ,,, (o o) -----------------------------ooo-(^)-ooo------------------------------------- U The years of peak mental activity are undoubtedly between the ages of four and eighteen. At four we know all the questions, at eighteen all the answers. ----------------------------------------------------------------------------- $$$ Disclaimer: opinions blah blah blah mine... $$$ *** From hcj@mazda.wavefun.com Thu Feb 2 17:41:54 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.9/930601.1506) id RAA21086; Thu, 2 Feb 1995 17:05:34 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA00393; Thu, 2 Feb 95 14:05:37 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA27692; Thu, 2 Feb 95 14:05:30 -0800 Date: Thu, 2 Feb 95 14:05:30 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9502022205.AA27692@mazda.wavefun.com> To: oesterei@hrz.ba-freiberg.de Cc: chemistry@ccl.net In-Reply-To: <199502021924.OAA16787@www.ccl.net> (message from Ralf Oestereich on Thu, 2 Feb 95 20:24:01 MEZ) Subject: Re: CCL:How to handle "COLLAGE" saved HDF files? Reply-To: hcj@wavefun.com >>>>> "Ralf" == Ralf Oestereich writes: Ralf> To make some hardcopies of SPARTAN images, we just tried to Ralf> grap the screen with COLLAGE. Now the question for us is, Ralf> how can we convert these HDF-format files, into a printable Ralf> postscript version? If you do a screen capture in Collage the picture is put into a whiteboard. From there you can save the image as postscript by choosing print image from the file menu, and then selecting save instead of print in the print dialog. This will open up another dialog to let you enter the filename. Hope this helps! -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From Don_Gregory@msi.com Thu Feb 2 17:43:47 1995 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.9/930601.1506) id RAA21475; Thu, 2 Feb 1995 17:23:18 -0500 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA14488; Thu, 2 Feb 95 17:25:20 EST Message-Id: <9502022225.AA14488@msi.com> Date: 2 Feb 1995 17:22:15 +0000 From: "Don Gregory" Subject: Re- CHARMM(m) Solvation To: "Comp. Chem. Listserver" Subject: Time:9:20 AM OFFICE MEMO Re: CHARMM(m) Solvation Date:2/2/95 On 2 Feb., McCarron from the UK wrote: "Could anybody out there tell me if it is possible to solvate using CHARMM. I know that CHARMM can recognise molecules already solvated but is it possible to solvate with this program like you can with AMBER say. Thanks for you help" ----------------------------------- Yes, indeed ....... CHARMM, the program is quite well suited for calculations on virtually all molecular systems. Although its original design was to take advantage of biomolecular systems, CHARMM has been used for materials, polymers, drug-design and many many other non-protein/nucleic-acid type systems. The CHARMM-Harvard and CHARMm-MSI force fields also, have been parameterized to be compatible with several well-validated water models, most notably the TIP3 model of Prof. Jorgensen. Solvation of molecules, most easily accomplished through the Quanta interface, can take the form of: periodic boundary systems, stochastic boundary systems and pressure-gradient calculations. In all these cases, it is trivial to solvate small molecular systems with a 15A or a 30A box of TIP3 waters (provided), or to solvate a subset of a much larger system with a sphere of water. We have recently been working up hexagonal cylinders of water to use with coiled peptide, and nucleic acid systems. Don Gregory Mgr. Life Science Applications, MSI From lohrenz@zinc.chem.ucalgary.ca Thu Feb 2 21:41:54 1995 Received: from zinc.chem.ucalgary.ca for lohrenz@zinc.chem.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id VAA24510; Thu, 2 Feb 1995 21:22:34 -0500 From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA26809; Thu, 2 Feb 1995 19:17:47 -0700 Date: Thu, 2 Feb 1995 19:17:47 -0700 Message-Id: <9502030217.AA26809@zinc.chem.ucalgary.ca> To: CHEMISTRY@ccl.net Subject: Dipole derivatives in G92 Dear CCL-friends, I'm sending the following question in behave of Vanitha, may be someone out there in the net can help us... My research entails vibrational circular dichroism (VCD) spectroscopy of biological molecules. I plan to use Gaussian92 for frequency analysis of the nucleotide bases. However, I have a problem finding the first derivative of the dipole moment with respect to a normal mode, i.e. I require the transition moment as input for a semi-empirical method of calculating VCD spectra. Dipole moment derivatives with respect to Cartesian coordinates are readily available on the Gaussian92 output but for my application I require the dipole moment derivative w.r.t normal modes. I will appreciate help or suggestions in this regard. Thank You Vanitha John Lohrenz Dept. of Chemistry University of Calgary 2500 University Drive, N.W. Calgary, Alberta, T2N 1N4 Canada email: lohrenz@zinc.chem.ucalgary.ca From Renate_Griffith@uow.edu.au Thu Feb 2 22:42:00 1995 Received: from wyrm.cc.uow.edu.au for Renate_Griffith@uow.edu.au by www.ccl.net (8.6.9/930601.1506) id WAA25173; Thu, 2 Feb 1995 22:03:38 -0500 Received: from uow.edu.au (ms-gw.uow.edu.au [130.130.68.33]) by wyrm.cc.uow.edu.au (8.6.9/8.6.9) with SMTP id OAA07604 for ; Fri, 3 Feb 1995 14:03:17 +1100 Message-ID: Date: 3 Feb 1995 14:02:46 +1100 From: "Renate Griffith" Return-Receipt-To: "Renate Griffith" Subject: medium sized heterocycles To: "COMPUTATIONAL CHEMISTRY LIST" X-Mailer: Mail*Link SMTP-MS 3.0.1 Dear netters, I am interested in the conformations of medium sized heterocycles at or around the global minimum and how to explore them. I am talking about 8-11 membered rings, containing one or two N and/or O atoms. I am also interested in controlling ring geometry via transannular interactions (e.g. H-bonding or N-carbonyl). Can anybody help me with references? Thank you Renate Renate Griffith Dept. of Chemistry University of Wollongong Australia email: r.griffith@uow.edu.au