From noy@einstein.sc.mahidol.ac.th Thu Mar 27 11:32:13 1997 Received: from einstein.sc.mahidol.ac.th for noy@einstein.sc.mahidol.ac.th by www.ccl.net (8.8.3/950822.1) id KAA22644; Thu, 27 Mar 1997 10:55:05 -0500 (EST) Received: (from noy@localhost) by einstein.sc.mahidol.ac.th (8.7.4/8.7.3) id WAA14674 for chemistry@www.ccl.net; Thu, 27 Mar 1997 22:30:40 -0700 From: "Dr. Teerakiat Kerdcharoen" Message-Id: <199703280530.WAA14674@einstein.sc.mahidol.ac.th> Subject: Getting Started with Gaussian To: chemistry@www.ccl.net Date: Thu, 27 Mar 1997 22:30:40 -0700 (GMT+7) In-Reply-To: <199703261553.KAA29504@alchemy.chem.utoronto.ca> from "E. Lewars" at Mar 26, 97 10:53:03 am Content-Type: text > H Y Jeong recently asked how he could get started using programs like > Gaussian. > > 1 General information on computational chemistry: > "Quantum Chemistry", by Ira N. Levine, 4th ed., Prentice Hall, 1991. > Very good introduction to QC, with problems (some answered). Chapters 15 and, > especially, 16 and 17 give a nice, brief overview of current computational May I added some here. A good new book just coming out to the shelf from Addison Wesley Longman Limited does worth your money. The title catches your eyes easily as "Molecular Modelling: Principles and Applications". The author is Andrew R. Leach and ISBN is 0-582-23933-9. Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: 2461381 FAX 2461381 Cellular: 01-4906089 E-mail: noy@einstein.sc.mahidol.ac.th, noy@atc.atccu.chula.ac.th Homepage: http://www.sc.mahidol.ac.th/noy/ Research: Computer Aided Molecular Design (CAMD) ----------------------------------------------------------------------------- From dgregory@msi.com Thu Mar 27 12:32:12 1997 Received: from bioc1.msi.com for dgregory@msi.com by www.ccl.net (8.8.3/950822.1) id LAA23088; Thu, 27 Mar 1997 11:57:28 -0500 (EST) Received: by bioc1.msi.com (5.64/0.0) id AA16175; Thu, 27 Mar 97 08:56:56 -0800 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma016171; Thu, 27 Mar 97 08:56:45 -0800 Received: from [146.202.16.2] by biff.biosym.com (4.1/SMI-4.1) id AA24260; Thu, 27 Mar 97 08:56:35 PST X-Sender: dgregory@146.202.0.225 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Mar 1997 08:57:40 -0800 To: chemistry@www.ccl.net From: dgregory@msi.com (Don Gregory) Subject: Re: CCL:How to prevent protein moving during dynamics? Hi Yun, If I read between your lines, my guess is that you have one very large sphere of surrounding water, with the protein in the middle ... ? and that when you did the SBMD the protein "diffused" to the boundary? Realize that the boundary potential has a lower-energy-well component in it, and that as one 'approaches' the boundary there is actually a bit of attraction, as there would be to numerous water molecules that the boundary is "representing" but then as one goes further and further into the boundary, there is a steep repulsive component, to keep molecules inside the boundary. So what you seeing is entierly .... understandable, if not desirable. I would think your only two alternatives at this point, would be to artifically restrain the protein, there are some ways one could think about doing this, but they all have the caveat of artificiallity. Some possibilities here might be the use of a droplet potential, or to add in a "dummy" atom at the center of your sphere, fix it, and put some weak distance constraints between it and some atoms near the center of the protein. Of course, you could also use a bigger sphere of water. Neither of these are optimal; in any case, it sounds like "starting" over in some manner will likely be necessary. Don Gregory At 6:08 AM 3/27/97, Yun Tang wrote: >Hi, everyone > >I tried to perform protein dynamics with deformable stochastic boundary >using CHARMM program. But during the dynamics process, the protein >gradually moved to the water sphere boundary and finally touched the >boundary. That meant I had to do it once more. > >Does anyone also meet this problem and how do you deal properly with it? >I mean how to prevent the protein moving during dynamics! Any >suggestions are appreciated! > >Thanks in advance and happy holiday to everyone! > >Yun Tang > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: yun.tang@csb.ki.se >-- Original Sender From: Address: yun.tang@csb.ki.se >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html Dr. Don Gregory (dgregory@msi.com) Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com From SMILLER@RARUSRAEXS1.prius.jnj.com Thu Mar 27 14:39:29 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id NAA23554; Thu, 27 Mar 1997 13:34:23 -0500 (EST) Received: by smtp-internet.jnj.com id AA06263 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Thu, 27 Mar 1997 13:34:24 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Thu, 27 Mar 1997 13:34:24 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Thu, 27 Mar 1997 13:34:24 -0500 Date: Thu, 27 Mar 1997 13:35:58 -0500 From: "Miller, Susan [PRI]" Subject: Summary of answers to QSAR question To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Dear CCL'ers, Following is a summary of the replies I received to my question about how long it should take to perform a QSAR analysis of 120 compounds. First is the original question and then come the answers. Thanks very much to all who replied. Dear CCL'ers' I am about to start doing some QSAR on a set of 120 compounds. How long should I expect it to take to overlay all 120 compounds and adjust their conformations, to achieve maximal overlap? A range of times or an approximate number of hours will make a fine answer. Thanks alot. Susan gee, wouldn't that depend on what software and methods you're using?  ___ _ http://ellington.pharmacy.arizona.edu/~bear O-topo-O (___ |.) bear@.pharmacy.arizona.edu 5' : : .* ___)OARING |_)EAR, UA Pharmacy 404, Tucson 85721 |'*. .*'| | Computer Modeling for Medicinal Chemistry; SAR CAMD | | *.,* | | | Protein/DNA Structural Biology; Cancer Biochemistry 3',DNA helix|.* Pharmacognosy, Herbs, Nutrition, Natural Dentistry '***' '**  It depends on a lot of things. If these are near analogs, where a common scaffold has the same numbering, a Sybyl spl (there is one called align, or at least I have one) will do a rough atom-to-atom alignment in a matter of a minute or so. If the structures are dissimilar, a manual use (in Sybyl) of the orient command will give you a very rough alignment in probably 30 or 40 minutes, depending on how good you are with the keyboard. If you want to do something fancy, like alignments based on similarity of the ESP. . .this gets to be time consuming. If you are also taking into account multiple conformations, or tweaking the alignment given a first-pass CoMFA-QSAR. . .you just have to try it. I infer from your address (prius.jnj) that you are with Johnson and Johnson. Debbie Loughney (sp?) is well versed in Sybyl. Have you discussed this with her? Viel Vergnuegung! Steve Bowlus Hi there, It depends on the machine power, qsar software, compound size, parameter selecting .....Generally, as I am doing now for about 100 compounds(MW. 300) using a PowerMac8100 with CAChe Project leader, one month or 500 hrs around is the common expense. Maybe I am lazy. Any QSAR topic I am interesting in. Yours, Canping Pan --------------------------------- E-mail: pan_canp@agr.kyushu-u.ac.jp Tel: 092-611-7122(H) 092-642-2858(O) Fax: 092-642-2864 http://133.5.200.42/pan.html Hi Susan, I am afraid your question is impossible to answer considering the background information you supplied. None. First you need a very well planned working strategy. Do you now anything about the target protein. That is, do you now anything about the ligand-target protein interactions? How flexible are your compounds? You need to perform conformational analyses on most of them. You must align low energy conformations from all compounds. This is the most crucial step in order to obtain a reliable 3D QSAR model. Having all compounds aligned the most time consuming part is over and the real fun begins. Cheers /jonas My company offers two products that you may find VERY useful. The first is AMPAC, a semiempirical quantum mechanical package along with an easy to use graphical user interface. The second is CODESSA, and advanced QSAR/QSPR program that does much of what you are currently doing manually automatically when paired with AMPAC. There are a number of reference papers in the literature describing the sorts of correlations that are possible, and one of them (#1 below) sounds somewhat like what you want to do. If you are interested and will send me your regular mail address, I'll be happy to send some propaganda in the way of brochures along. Also, perhaps we can arrange a demo if you think that you might be further intrigued. Let me know. Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dear CCL'ers, You have all rightly pointed out that I did not provide sufficient background information for an answer to my question. I will provide it now (I hope): I am doing everything manually, from the overlays to the conformational searches. The compounds I am aligning fall into about half a dozen structural categories (by my reckoning), within which there is not great structural variation but among which there is little similarity. There are large flat fused ring structures and spiro compounds, single phenyl rings with long aliphatic chains on either side (in some cases branched, in others, not) and pairs and larger sets of phenyl and non-aromatic rings connected by aliphatic chains and other moieties. I hope this clarifies the earlier question somewhat. Thanks for your replies, both future and those already sent. Susan -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: SMILLER@RARUSRAEXS1.prius.jnj.com -- Original Sender From: Address: SMILLER@RARUSRAEXS1.prius.jnj.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html Dear Susan, Please, post a summary with your answers. Which software are you using to do the QSAR study? Thanks, Ezequiel If you know the corresponding points then this is pretty easy. The cheapest way is to do ensemble distance geometry. I would use the most constrained analogue of each class. Generate 100 ensembles with that contain the chosen member of each class. Minimize the structures. Then see which ensembles (1) still match & how well and (2) contain mainly low energy conformations. You will discover either that you have only a few solutions (good) or 50 or so different solutions which will tell you that you will never have a unique choice of conformations so you might as well just pick one set and move on. Ensemble distance geometry is available in DGEOM from QCPE. Sheridan, R. P.; Nilakantan, R.; Dixon, J. S.; Venkataraghavan, R., J. Med. Chem. 1986, 29, 899-906. "The Ensemble Approach to Distance Geometry: Application to the Nicotinic Pharmacophore". If you don't know what atoms correspond in the different structures, you can run a bunch of DGEOM runs to see which give solutions. Or, you can use DISCO, an option with Sybyl. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A., J. Comput.-Aided Mol. Design 1993, 7, 83-102. "A Fast New Approach to Pharmacophore Mapping and its Application to Dopaminergic and Benzodiazepine Agonists". It shouldn't take you a month to do what you want, except that you are apparently learning in the process with no good tutor. How do you plan to do the QSAR? Yvonne Martin, Senior Project Leader Computer Assisted Molecular Design Project D-47E, AP10 2fl Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-3500 Phone: 847 937-5362 FAX: 847 937-2625 yvonne.c.martin@abbott.com Susan, For the situation you have described, I highly recommend SEAL, an automatic alignment program, available from QCPE for a small fee. Forget manual alignments - it will take forever! With SEAL, you can align all 120 of your molecules (even if you have ~20 conformations of each) in <= a few hours. Good luck. Mary /*************************** * * * Mary Bradley * * Senior Research Scientist* * Rhone-Poulenc Ag Company * * * * bradleym@mindspring.com * * * ***************************/ *********************************** Mary Bradley * email: mbradley@mindspring.com * fone & fax: (919) 572-6599 * *********************************** Dear Suzan I don't know what you mean by hand... Could you tell me what are the modelling softwares available in you lab ? I see two problems to face : Conformer generation (it seems that you have very flexible compounds) and conformer fitting. I would suggest you to start with the more rigid compounds, do a conformational search (systematic, random, high temperature dynamic as you want or as you can). Keep structures in a range of 10-20 kCal above the minima (don't forget to investigate ring conformation). Then make hypothesis on what would be the pharmacophore (charged atom, hydrogen donnors or acceptors, aromatics, lipophilic groups etc...) or any common points available in your series or reported in literature. Then measure some key distances between these elements and try to cluster the molecules according to these parameters (with SAS) or make some sorts with excel to identify the common pharmacophore if you don't have any specific softwares to do that. Once you have identified the best clusters then you can superimpose the best conformations. Concerning the more flexible molecules, don't spend time to generate conformers but simply check that you can simply superimpose one reasonable conformation to the previously identified pharmacophore. To my opinion, and without any additional information, you have to plan some months to do the job. Hope this helps Don't hesitate to contact me for help Francois ------------------------------------------------------------------------ -- Dr. Francois CROIZET - Riom Laboratoires CERM - Chemistry Dept. (CMC) - ZI de la Varenne, Rue H. Goudier, BP 140 - 63203 RIOM Cedex - FRANCE - Phone: (33) 473 33 49 70 - Fax: (33) 473 33 49 97 E-mail: f.croizet@organon.akzonobel.nl ======================================================================== == For automated overlay of two molecule with conformational flexibility on PC, PowerFit may be useful. You can go to our web site to download a fully functional program to evaluate. Currently only Windows 95 and NT version is available for download. For automated overlay of two molecule with conformational flexibility on PC, PowerFit may be useful. You can go to our web site to download a fully functional program to evaluate. Currently only Windows 95 and NT version is available for download. Ms. (Dr.?) Miller: For the past few days, I have been following with interest your postings to the CCL concerning QSAR. (BTW, I haven't seen (most of) the responses to you show up in my mail, so I'm assuming they're going directly to you.) Since I do molecular modeling and algorithm design, I haven't felt competent to comment on your questions. After your last posting, however, I feel compelled to register extreme surprise (and to stick my nose in where it doesn't belong :-). Why, pray tell, would your mentor even suggest doing _all_ of the overlays by hand??? There is certainly value to doing a small, random set of overlays by hand, just to confirm that the results make sense. However, if you're needing to do anything more than a couple of handfuls of compounds, noninteractive fitting seems the only way to go. Otherwise, you end up wasting enormous amounts of human time doing things a mindless computer was invented for. On the other hand, if you're using Tripos software, I guess noninteractive isn't really a choice anyways? Ah well, good luck with your project. I hope you're able to finish in something approximating a reasonable amount of time. Sorry for butting into the middle of your more substantive discussion with people who actually do QSAR... Marti Head %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Martha S. Head, Ph.D. (Marti) Center for Advanced Research in Biotechnology 9600 Gudelsky Drive Rockville MD 20850 voice: (301)738-6104 email: mhead@indigo18.carb.nist.gov %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hi all, Thanks again for all of your responses. I will post a summary in a couple of days when the discussion is over. All of the responses I've received so far have come to CCL and not to my personal mailbox, but if it is desired, I can still post a compilation of the responses. I forgot to mention 2 very important facts: 1) I am using SYBYL and have no access to anything else, save the free software on the net. I cannot use that however, for the second reason. 2) My mentor insists that I do the overlays by hand, that is, by using the fit module in SYBYL and picking points, with the mouse, to fit. I must also do torsion adjustments by hand, that is, by choosing a torsion angle for each bond and applying it, using either the twist widget in the upper left corner of the screen or the modify torsion command. Susan -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: SMILLER@RARUSRAEXS1.prius.jnj.com -- Original Sender From: Address: SMILLER@RARUSRAEXS1.prius.jnj.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html Susan, The superimposition procedure is performed due to that the 3D structure of the target protein is not known. You seek atoms or mutual points on your ligands that are most likely to interact with target protein. However, very often your fits will be much better if you also allow extension vectors to act as a fit point. For example, a basic nitrogen may interact through its lone pair of electrons or, if it is protonated, through the proton. Therefore, if you apply extension vectors in the direction of the lone pair of electrons , and use this vector as a fit point, much more reliable fits will occur. You use a UNIX machine and I suggest that you use Apollo or a similar program for this. Even SYBYL has a module. Your mentor does not allow you to perform conformational searches on your ligands? Then why bother at all. This is, one of the most crucial steps in 3D QSAR, especially if your ligands are flexible. In SYBYL I suggest you to use the random search procedure! The conformational search and the alignment proecedures are tedious and cost a lot of time, but must be performed rationally and thoroughly. Succes /jonas ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Jonas Nilsson e-mail: j.nilsson@farm.rug.nl Univ. Centre for Pharmacy tel: +31(0)503633302 Dept. of Med. Chemistry fax: +31(0)503636908 Antonius Deusinglaan 1 NL-9713 AV Groningen The Netherlands http://pc131.farm.rug.nl/main.htm ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ (In reply to your message dated Tuesday 11, March 1997) -- Something of interest for QSAR work. Accord for Excel can be used for structure relationships and Activities. Check out WWW.synopsys.co.uk Take care, all. Susan From jtgolab@amoco.com Thu Mar 27 18:32:13 1997 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id RAA25093; Thu, 27 Mar 1997 17:45:35 -0500 (EST) Received: by interlock.amoco.com id AA27857 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Thu, 27 Mar 1997 16:45:34 -0600 Message-Id: <199703272245.AA27857@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Thu, 27 Mar 1997 16:45:34 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Thu, 27 Mar 1997 16:45:34 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Thu, 27 Mar 1997 16:45:34 -0600 From: jtgolab@amoco.com (Joe Golab) Date: Thu, 27 Mar 1997 16:44:42 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii 3/27/97 RE: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" >-- Original Question >! Dear CCL: >! >! Recently, we upgraded our Silicon Graphics equipment to IRIX 6.2. After >! that, Xmol stopped working (% xmol - Exec format error) because Xmol uses >! the COFF binary format. According to Xmol's creators (Minnesota's SC), >! "There are not plans to produce a new XMol distribution". >! >! We have been looking for an alternative to Xmol. So far, we haven't had >! much luck to duplicate Xmol's "Extras/Animate" feature. We have found that >! feature very useful when looking at optimization runs, IRC runs, etc. The >! animation button basically reads and displays a series of geometries from an >! Xmol input file. >! >! Can anyone suggest an alternative software product for UNIX machines? >! We have tried Rasmol and have not had any luck getting it to do animation >! using a series of separate geometries. (Which should not be taken as a slam >! to Rasmol which we have found useful for Web presentations.) >! >! If any replies are received, I'll post the summary. Thank you. >! >! -- >! >! :Joe >! jtgolab@amoco.com >! (630) 961-7878 >-- Executive Summary 1) Source Code to Xmol is not available (to the best of my knowledge). It was only distributed via executable code. I (for one) wish one of the commerical software vendors would investigate the possibility of distributing a working copy of Xmol. As far as I know, MSC has no plans for it beyond what is on their web site now. (Hint, Hint, Knudge, Knudge, Wink, Wink - Know what I mean?) 2) Suggested Replacements a) VMD - http://www.ks.uiuc.edu/Research/vmd/ b) MOLDEN - http://www.caos.kun.nl/~schaft/molden/molden.html c) Chime - http://www.mdli.com/chemscape d) gOpenMol - http://laaksonen.csc.fi/gopenmol/gopenmol.htmls >-- Response *> Hi again Joe. I don't use Xmol, but would the MOLDEN program do what *> you need? I use it to visualize geometry optimizations, vibrational *> frequencies, and orbitals from Gaussian and sometimes GAMESS. It's *> free and has a web page: *> http://www.caos.kun.nl/~schaft/molden/molden.html *> *> Good luck! *> *> ---------------------------------------------- *> Dr. Karl K. Irikura *> Physical and Chemical Properties Division *> National Institute of Standards and Technology *> Gaithersburg, MD 20899 *> voice: 301-975-2510 fax: 301-975-3670 *> e-mail: karl.irikura@nist.gov *> ---------------------------------------------- >-- Response *> try using Chime as a plugin of a web page. It allows animations. *> You only will have to set up a web page to do the embedding. *> *> Chemscape Chime is free downloadable from http://www.mdli.com/chemscape *> *> Rene P.F. Kanters *> Chemistry Project Specialist *> Chemistry Department *> University of Richmond VA 23173 *> *> phone: (804) 287-6873 *> email: rkanters@richmond.edu *> www: http://www.richmond.edu/~rkanters *> http://www.science.richmond.edu/~kanters >-- Response *> You might want to try VMD, just released to the public on Mar 25. It's *> homepage is http://www.ks.uiuc.edu/Research/vmd/ *> *> David E. Reichert, Ph.D. *> Mallinckrodt Inst. of Radiology *> Div. Radiation Sciences *> phone: (314)362-8461 *> fax: (314)362-9940 *> e-mail: reichertd@mirlink.wustl.edu >-- Response *> I use vmd to display dynamics (results from MD and normal modes). *> I think vmd can use Xmol's xyz files, however I never tried that. *> Instead, I wrote a little program that generates dcd files that *> vmd can read. You are welcome to have it, if you want. *> I found that vmd makes very fast and very pretty animation. *> I you don't know where to find vmd on the net, I cal dig it up for you. *> *> Hope that helps, Gert *> *> Gert von Helden *> Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands *> e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311 >-- Response *> Did you tried the molden software ? *> I use it on IRIX6.2 but you should have gaussian output. *> Is it your case *> *> Dorothee Berthomieu *> ************************************************** *> Laboratoire des Materiaux et Procedes Membranaires *> UMR CNRS 5635 *> Ecole Nationale Superieure de Chimie de Montpellier *> 8, rue de l'Ecole Normale *> 34296 MONTPELLIER cedex 5 *> Tel : (33) 467 14 43 40 *> Telecopie : (33) 467 14 43 47 *> email : bertho@crit1.univ-montp2.fr *> http://www.dr13.cnrs.fr/lmpm/fequ.html#DEPOCVD >-- Response *> Have you tried MolDen? It can read various file types (e.g. Gaussian *> output) and animate things like structures and vibrational modes. *> *> Nick *> *> ============================================================================ *> Nicholas A. Nystrom, Ph.D. Pittsburgh Supercomputing Center *> Scientific Specialist Mellon Institute Building *> email: nystrom@psc.edu 4400 Fifth Avenue *> voice: +1 412-268-1592 fax: -5832 Pittsburgh, PA 15213 USA *> ============================================================================ >-- Response *> Can't you get the xmol source code? All you should *> need to do is to rebuild the executable. If the program *> is being distributed form an academic center, I would *> be surprised if they would not hand out the source. *> *> Good luck, *> *> Randy *> *> All opinions expressed here are mine, not my employer's *> *> ///////////////////////////////////////////////////////////////////////// *> \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // *> \\ Tripos, Inc. | : zauhar@fastrans.net // *> \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // *> \\ St. Louis, MO 63144 | // *> ///////////////////////////////////////////////////////////////////////// *> ** ** *> ** "If you have conceptions of things that you can have no conception ** *> ** of, then the conception and the thing appear to co-incide." ** *> ** --- C.G. Jung ** *> ************************************************************************* >-- Response *> Joe, I assume the source for XMol was never distributed? Does anybody own *> it currently? If they're not going to make a new distribution, what's *> happening to the program? *> *> All that's required is a recompile on an appropriate SGI... *> *> Joe *> *> -- *> *> Joe Leonard Phone: +1 314 647 8837 x3204 *> Tripos, Inc. Fax: +1 314 647 9241 *> 1699 S. Hanley Rd. email: jle@tripos.com *> St. Louis, MO 63144 USA after-hours: jle@world.std.com >-- Response *> We went through exactly the same process. We're presently using the package *> VMD. You can obtain a copy via http://www.ks.uiuc.edu/Research/vmd/ . It can *> read in multi-frame XYZ files. Might be worth a try.... *> *> Regards, *> Mike *> *> ------------------------------------------------------------------- *> | Mike Fearn, Tel : UK (01684) 896536 | *> | Room PA101, Fax : UK (01684) 896150 | *> | D.R.A, Malvern, | *> | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | *> ------------------------------------------------------------------- >-- Response *> There are certainly a lot of options. Let me suggest one further: *> *> The gOpenMol program at: *> *> http://laaksonen.csc.fi/gopenmol/gopenmol.htmls *> *> Regards, *> *> -leif laaksonen *> *> ------------------------------------------------------------------- *> Leif Laaksonen | *> Center for Scientific Computing | Phone: 358 9 4572378 *> P.O. Box 405 | Mobile: 358 400425203 *> FIN-02101 Espoo | Telefax: 358 9 4572302 *> FINLAND | Mail: Leif.Laaksonen@csc.fi *> -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- >-- Response *> This seems to be a common question lately as more and more *> people upgrade to 6.x . You might want to look at our visualization *> program, VMD, at http://www.ks.uiuc.edu/Research/vmd/ . It was *> developed for, amoung other things, the visualization of MD *> trajectories. *> *> I doesn't read XYZ files directly, but if you have Babel *> installed (http://mercury.aichem.arizona.edu/babel.html) it VMD *> will call it and to the conversion to a set of PDB files automatically, *> then read them in. To the user, you wouldn't even notice the exchange. *> *> Andrew *> dalke@ks.uiuc.edu -- :Joe jtgolab@amoco.com (630) 961-7878 +----------------------------------------------------+ | Profanity - the one language all programmers know. | | After all, why do you think they call it a cursor? | +----------------------------------------------------+