From RCMAH@bunyip.ph.rmit.edu.au Wed Apr 10 03:45:41 1996 Received: from peladon.rmit.EDU.AU for RCMAH@bunyip.ph.rmit.edu.au by www.ccl.net (8.7.1/950822.1) id DAA25767; Wed, 10 Apr 1996 03:43:05 -0400 (EDT) Received: from bunyip.ph.rmit.edu.au (bunyip.ph.rmit.EDU.AU [131.170.248.94]) by peladon.rmit.EDU.AU (8.7.5/8.6.9) with SMTP id RAA29245 for ; Wed, 10 Apr 1996 17:42:45 +1000 (EST) Received: from BUNYIP/SMTPQUEUE by bunyip.ph.rmit.edu.au (Mercury 1.13); Wed, 10 Apr 96 17:48:28 +1100 Received: from SMTPQUEUE by BUNYIP (Mercury 1.13); Wed, 10 Apr 96 17:48:08 +1100 From: "BERT HOVELING" Organization: RMIT Applied Physics To: chemistry@www.ccl.net Date: Wed, 10 Apr 1996 17:48:02 EST-10 Subject: Cray Unichem X-Confirm-Reading-To: "BERT HOVELING" X-pmrqc: 1 Return-receipt-to: "BERT HOVELING" Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: Hi CCL Participants, I am interested in obtaining a list of CCL participants, and any others, who are current users of Cray's Unichem Software. I will summarise the list for all after a reasonable period of response time. Regards to All. Bert Hoveling Dr.A.W.(Bert) Hoveling Department of Applied Chemistry, R.M.I.T. 124 La Trobe Street Melbourne, Victoria, Australia, 3001 Phone: (03) 660-2117 Facsimile: (03) 639-1321 E mail: hoveling@rmit.edu.au From landman@motown.detroit.sgi.com Wed Apr 10 08:45:43 1996 Received: from sgi.sgi.com for landman@motown.detroit.sgi.com by www.ccl.net (8.7.1/950822.1) id IAA29254; Wed, 10 Apr 1996 08:28:52 -0400 (EDT) Received: from motown.detroit.sgi.com by sgi.sgi.com via ESMTP (950405.SGI.8.6.12/910110.SGI) for <@sgi.com:chemistry@www.ccl.net> id FAA17978; Wed, 10 Apr 1996 05:28:52 -0700 Received: from motown.detroit.sgi.com by motown.detroit.sgi.com via SMTP (950511.SGI.8.6.12.PATCH526/911001.SGI) for id IAA02113; Wed, 10 Apr 1996 08:28:50 -0400 Date: Wed, 10 Apr 1996 08:28:50 -0400 (EDT) From: Joseph Landman To: chemistry@www.ccl.net Subject: Molecular Inventor, Java, and other WWW developments In-Reply-To: <9604090931.ZM13496@xhost2.tripos.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Given my affiliation, I have been staying out of this debate, though I have my own personal opinions on this.. On Tue, 9 Apr 1996, Paul Weber wrote: [...] > "News") at www.sgi.com. I'm also surprised to see the attention focused > just on Java -- if all you want to do is look at a molecule, you might > consider VRML as well as Molecular Inventor for getting a much improved > display quality. VRML and MI formats are pretty easy to write too, so > general support in the future seems to be a good bet. > This is true. I wrote a quick xyz-Open Inventor translator about 6 months ago to show my GaAs systems. I halted any forther work after seeing molecular inventor demos, figuring on taking advantage of it when released. It is good database format for display, and is non-proprietary (in the sense of OpenInventor being *open*, and Template Graphics and others having ports to MANY platforms, including all flavors of Windows, Linix, possibly OS/2, Mac, etc) I believe that MI may solve some of the thornier issues about portability of models, including the connectivity data, between formats and programs. Actually I am of the opinion that the Molecular Browser/Interactor is somewhat seperate from the question of the data type. There is no doubt as to the potential for a Java app/applet to do a reasonable job at browsing, rotating, etc a molecule. However, the implementation still needs to be done, and levels of functionality need to be defined. What is good for the undergrad may not be good for the graduate student/researcher/professor. So, is there any support for defining quantised levels of functionality in a browser? e.g: Level 1) Browsing: rotation, translation, panning. Advantages are that this is small and fast, without excess code needed for operations that will not be performed at this level. Intended for large scale audiences who simply need to see the molecule. Level 2) Interaction: All of level 1, plus atom selection, distance and angle calculation, marking sub-parts (chains/ribbons/etc) of larger molecules. Level 3) All of level 2 including hooks into your favorite renderer, as well as trajectory information for dynamics runs, and much more. (this is quite rough, feel free to hack away) > Now about Java - > > The download times are a drawback that many have noted, and many are > working on. Downloading the classes once and storing locally is > probably the best bet, as long as the application remembers to check > to see if it is still up to date. We could set up a directory site at CCL that the application checks at least once a month for latest versions of Java code. [...] > vendors. Thus, a "plug and play" of applications. The real issue then > is will there be a common data format to drag and drop between applets? > Again, I think the Molecular Inventor format from SGI comes the closest > to what we could use (and Tripos is using it, as well as MSI and probably > other vendors, too). Given the Template Graphics port (as well as others) to many platforms, one should be able to do a drag and drop between the viewer and their word processor (I am assuming OLE or OpenDoc style linkage). Most of SGIs own productivity tools are like that now (in terms of being able to import/export these open formats) and this is certainly a benefit in my opinion. [...] > I think that it is a good time for the community to search for acceptable > standards, such as SGI's Molecular Inventor, Tripos's SLN, DayLight's > SMILES, or the PDB (yuck). The chemistry community could then promote the > use of these standard formats by all software producers, whether garage-shop, > grad student, or public company. > Paul L. Weber, Ph. D. > Vice President, Product Development Phone: 314 647 1099 > Tripos, Inc. Fax: 314 647 9241 > 1699 S. Hanley Rd > St. Louis MO 63144 USA Email: weber@tripos.com +-----------------------+----------------------------+ / | Joe Landman | +1 810 615 2169 voice | / | Systems Engineer | +1 810 478 3181 fax | / | Silicon Graphics Inc. | x 5-7670 corporate | / | 24155 Drake Road, | landman@detroit.sgi.com | / | Farmington MI 48335 | Mail stop DMR 225 |/ +-----------------------+----------------------------+ From gmercier@helix.nih.gov Wed Apr 10 11:45:50 1996 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.7.1/950822.1) id LAA02616; Wed, 10 Apr 1996 11:09:32 -0400 (EDT) Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.13/8.6.12) with SMTP id LAA17171 for ; Wed, 10 Apr 1996 11:09:32 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 10 Apr 1996 11:23:36 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: Dendrimer MD/MM, Coordinates. Hi! I am interested in MD/MM of dendrimers. I have a few questions since I am a neophyte in this area :(. Specifically, I am looking for software/algorithms that people may use to generate coordinates and perform these simulations. As described below, common programs like amber and charmm have their limitations when applied to these molecules. Although I have some experience with programs like amber and charmm, it is clear that these programs expect linear polymers. Unfortunately, the starbust dendrimers of PAMAM are branched polymers with two branches off the tail end. / C ------------N / \ -C-----N \ / C-----------N \ So, when you have a repeating unit like / -C------N \ and try to specify the sequence you need a mechanism to tell the program that two residues are attached to one! In amber the link program does not allow for this, nor the sequence command allows for this under charmm. A potential work around can be develop using patches in charmm. In principle this means that you could start your sequence from generation g0, that is, with a core and its first branches, then patch along to add the repeating units. / C----------N / / \ core = N---C---N \ \ / C-------------N \ Have two patches, one for each branch point along the N's. Then loop again moving to the next set of "residues". The looping mechanism is tricky, but can be simplified by specifying the branches of the core using the segid, and each repeating unit by a residue number. If the RTF has internal coordinates specified, this can be used to generate coordinates! (Thanks to Dr. Langley for reminding me of charmm patches!) Has anybody implemented this in a charmm script and is willing to share it? Is there another, possibly simpler solution using other software or even within charmm. Thanks for your help! Bye Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov >From fred@org.chem.uva.nl Wed Apr 10 12:08 EDT 1996 Received: from org.chem.uva.nl for fred@org.chem.uva.nl by www.ccl.net (8.7.1/950822.1) id MAA04845; Wed, 10 Apr 1996 12:08:53 -0400 (EDT) Received: from [145.18.130.53] (lbo1dip53.chem.uva.nl [145.18.130.53]) by org.chem.uva.nl (8.6.12/8.6.12) with SMTP id SAA17166 for ; Wed, 10 Apr 1996 18:02:34 +0200 Message-Id: Mime-Version: 1.0 Date: Wed, 10 Apr 1996 18:09:59 +0100 To: chemistry@www.ccl.net From: fred@org.chem.uva.nl (Fred Brouwer) Subject: conference announcement update Content-Type: text/plain; charset="us-ascii" Content-Length: 3226 Status: R CONFERENCE MOLECULAR MODELLING OF CHEMICALS AND MATERIALS Amsterdam, The Netherlands, 9-10 September, 1996 Society's demands for affordable chemicals and materials with novel or enhanced performance characteristics continue to grow as exciting new application areas are recognised, and the requirements in existing areas become increasingly more stringent. Molecular modelling and simulation techniques have an important role to play in these developments by helping to provide a more focussed, molecular-level understanding of chemical products and processes, which in turn can help to guide future experimental work. This meeting, organised by the Molecular Graphics and Modelling Society and the University of Amsterdam, will bring together theoreticians and experimentalists from a variety of relevant fields to discuss molecular modelling approaches in chemicals and materials research, and is expected to be of value to scientists in industry and academe alike. Topics covered by the meeting will include: - Catalysis and Surfaces - Fluids and Interfaces - Polymers Speakers will include: Prof. E.J. Baerends (Amsterdam), Prof. J.H.R. Clarke (UMIST), Dr. J. Gale (London), Prof. W.A. Goddard (Caltech), Dr. F. Muller-Plathe (ETH, Zurich), Prof. K. Roberts (Strathclyde), Prof. R. Van Santen (Eindhoven), Dr. B. Smit (Shell) and Prof. D. Tildesley (Imperial, London) Organising Committee : Dr. M.A. King (Shell) Chairman; Dr. E.A. Colbourn (Oxford Materials Ltd.); Dr. M.G.B. Drew (University of Reading); Dr. A.M. Brouwer (University of Amsterdam) Local Organiser; Dr. R. Peschar (University of Amsterdam) Local Organiser Program The program will consist of invited lectures and oral presentations. On both days there will be a session of ca. three hours which will include buffet lunch, poster session and a commercial exhibition, all in the same location. Abstracts (one page A4, ready for reproduction) of contributed talks or posters should be sent to Dr. A.M. Brouwer at the address below. If you wish to present your work orally please ensure that your abstract is in our possession before July 1, and please add a brief description of your position and scientific career. The selection of oral presentations will be made before July 30. The committee will favour contributions from younger scientists. Registration The conference fee is DFl. 300 for regular participants, DFl. 175 for students. For registration after July 1 the fee is increased by DFl 50. To qualify for the reduced rate students must include a letter from their research supervisor. A limited number of student bursaries will be available. The registration fee includes a book of abstracts, lunches, coffee and tea during breaks, and an informal dinner on monday evening. Registration and hotel reservation forms are available at the: Conference WWW page: Http://krop.chem.uva.nl/mgms/ or will be sent upon request at the (E-mail) adress below. Send abstracts and registration form to: Dr. A.M. Brouwer University of Amsterdam, Laboratory of Organic Chemistry Nieuwe Achtergracht 129, NL-1018 WS Amsterdam, The Netherlands Fax 31 (0)20 5255670, E-mail: mgms@chem.uva.nl >From huang@mazda.wavefun.com Wed Apr 10 21:37:00 EDT 1996 From: "Wayne Huang" Message-Id: <9604101723.ZM8150@mazda.wavefun.com> Date: Wed, 10 Apr 1996 17:23:47 -0700 Reply-To: huang@wavefun.com To: CHEMISTRY@www.ccl.net, sparlist@mazda.wavefun.com Subject: 96.06.12 Computational Chemistry Workshops Hello all, Workshop time again! We are continuing to offer three-day intensive Computational Chemistry Workshops to our chemistry community. Due to the popular demand on June workshop, I have scheduled a second workshop in June (June 26-28), in addition to the one in June 12-14. Drop me a line at workshop@wavefun.com for a complete brochure. Meanwhile, happy computing! --Wayne Attachment is the information on the workshop and course materials. The complete brochure can be sent via fax/mail upon request. ====================================================================== ------------------------------------ | COMPUTATIONAL CHEMISTRY WORKSHOP | ------------------------------------ Intensive 3-day workshops focus on application of modern electronic structure methods to chemistry. Lectures will describe underlying theory, assess performance of modern electronic structure methods, outline practical strategies for doing calculations, and illustrate results of applications to diverse chemical problems. Laboratories provide hands-on experience using a wide selection experiments, as well as ample time to explore your own chemistry. Visualization and animation will also be presented for both educational demonstration and research presentation. Here are the summary of workshop information: _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ COMPUTATIONAL CHEMSITRY WORKSHOPS _/ _/ _/ _/ Format: 3-day intensive workshop on electronic structure _/ _/ methods and applications, and hands-on molecular _/ _/ modeling laboratory on individual workstations. _/ _/ It will provide: _/ _/ _/ _/ o Concise summary of modern electronic structure _/ _/ methods _/ _/ o Assessment of range and performance of their _/ _/ applications _/ _/ o Hands-on experience in molecular modeling _/ _/ o Graphical Analysis of results _/ _/ o Visualization and animation of structures and _/ _/ reactions _/ _/ _/ _/ Schedule: June Workshop (1): June 12-14, 1996 _/ _/ June Workshop (2): June 26-28, 1996 _/ _/ September Workshop: September 4-6, 1996 _/ _/ November Workshop: November 6-8, 1996 _/ _/ _/ _/ Instructors: Lecture Section - Dr. Warren Hehre _/ _/ Lab Section - Dr. Wayne Huang _/ _/ _/ _/ Location: Wavefunction, Inc. Irvine, California, USA _/ _/ _/ _/ Fee: $1000 (50% off for academics, $500), which _/ _/ includes course registration, five computational _/ _/ textbooks and one animated CD-ROM, all breakfasts _/ _/ and lunches. _/ _/ _/ _/ Textbooks: o "Chemistry with Computation", Warren Hehre & _/ _/ Wayne Huang, 1995. _/ _/ _/ _/ o "A Laboratory Book of Computational Organic _/ _/ Chemistry", Warren Hehere, Alan Shusterman & _/ _/ Wayne Huang, 1996. _/ _/ _/ _/ o "Experiments in Computational Organic Chemistry"_/ _/ Warren Hehre, Lonnie Burke, Alan Shusterman and _/ _/ William Pietro, 1993. _/ _/ _/ _/ o "A Short Course in Modern Electronic Structure _/ _/ Methods", Warren Hehre, 1995. _/ _/ _/ _/ o Educational CD-ROM "SpartanLive - Visualization _/ _/ of Chemical Structures and Reactions", Tom Hehre_/ _/ Lonnie Burke, Wayne Huang & Warren Hehre, 1995. _/ _/ _/ _/ o "Practical Strategies for Electronic Structure _/ _/ Calculations", Warren Hehre, 1995. _/ _/ _/ _/ Information: Workshop WWW: http://www.wavefun.com/workshop.html_/ _/ or contact Wayne Huang for further information _/ _/ including detailed brochure and course curriculum._/ _/ Tel: (714)955-2120 Fax: (714)955-2118 _/ _/ E-mail: workshop@wavefun.com _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/