From doelz@comp.bioz.unibas.ch Wed Feb 10 14:50:31 1993 Message-Id: <199302101250.AA16872@oscsunb.ccl.net> Date: Wed, 10 Feb 93 13:50:31 +0100 From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) To: chemistry@ccl.net Subject: Molecular Graphics and the Design of Bioactive Compounds Announcement of the 2nd Circular and Call for Papers /--\ ================================ \--/ || ... Molecular Graphics Society \ / \ : : \ / \. ... : 12th Annual Conference | . . : | . ...: ================================ / \ / : : / \ / :..: || Interlaken, June 8-11, 1993 /--\ SWITZERLAND \--/ Molecular Graphics and the Design of Bioactive Compounds Theme of the Conference The 12th Annual Conference of the Molecular Graphics Society will focus on the Methods and Results in the Computer Aided Design of Bioactive Molecules, with emphasis on the crucial role which Molecular Graphics plays in the visualization and interpretation of data in this field. The Conference sessions will be centered around the following four general topics 1) Molecular Design (methodology and applications, two sessions) 2) Structure-Guided Design: (a) based on X-ray crystallography (b) based on NMR spectroscopy 3) Databases: Use and Applications 4) Structure-Property Correlations Scientific Programme _____________________________________________ The topic of the conference, "Molecular Graphics and the Design of Bioactive Compounds" has been divided into six half-day sessions, each covering a particular subtopic which is opened by a main lecture followed by a number of selected oral presentations. A long lunch breack is scheduled to enable participants to visit the scientific poster session and the commercial software/handware exhibition. Monday, June 7 afternoon Registration evening Opening of Conference and Welcome Address H.P. Weber, chairman of the Organizing Committee Opening Lecture: Molecular Graphics and Structure Design K. M|ller, F. Hoffmann-La Roche AG, Basel (CH) Welcome Cocktail Tuesday, June 8 morning Session 1: Molecular Design I Main Lecture: 3D Models of Dopamine, Adrenaline, Serotonine, Acetycholine and Mammalian Opsine Receptors Marcel Hibert, Marion Merell Dow, Strasbourg (F) afternoon Session 2: Structure-Property Correlations Main lecture: Hydrophobic Interactions and CoMFA using HINT D.J. Abraham, Virginia Commonwealth University, Richmond VA (USA) Wednesday, June 9 morning Session 3: Structure-Based Design (using NMR and related methods) Main Lecture: At Last Coupling Constants Again - Structure and Dynamics of Peptides and Proteins by NMR and MD Calculations H. Kessler, Technische Universitdt, M|nchen (D) afternoon Conference Excursion, Poster and Commercial Exhibition (optional) Thursday, June 10 morning Session 4: Structure-Based Design (using X-ray Crystallography) Main Lecture: Protein Structure and Drug Design T.L. Blundell, Birkbeck College, London (UK) afternoon Session 5: Databases Main Lecture: The Information Explosion: How Can we Cope? P. Murray-Rust, Glaxo Research, Greenford (UK) evening Conference Dinner Friday, June 11 morning Session 6: Molecular Design II Main Lecture: CAVEAT, TRIAD, and ILIAD P. Bartlett, University of California, Berkeley, CA (USA) Closing Lecture: Computer Simulations of Biomolecules: Improvements in Methodology for Searching Conformational Space and Prediction of Molecular Properties W. van Gunsteren, ETH, Z|rich (CH) afternoon Closing of Conference and Farewell Drink A commercial exhibition of relevant hardware and software will be organized and accessible during the Conference. Scientific Advisory Board Organizing Committee Hoeltje H.D., Berlin Breckenridge R., Basel Karplus M., Harvard Doelz R., Basel Mueller K., Basel Karfunkel H., Basel Richards G., Oxford Van de Waterbeemd H., Basel Silvestre J., Lyon Weber H.P., Basel (Chairman) Thornton J., London Tollenaere J., Beerse Weber J., Geneva Attendance and Call for Contributions Please indicate your interest in attending the Conference and to present a paper by requesting the application form from the conference secretariat 12th Annual Conference of the MGS P.O. Box 6, Clarastrasse 57 CH-4005 Basel, Switzerland Tel. ++41-61-691 51 11 Fax. ++41-61 691 81 89 (Deadline for Abstracts: March 31, 1993) Location and Date of the Conference Interlaken is located in the beautiful alpine Bernese Oberland, nested between the two lovely lakes of Thun and Brienz in breathtaking proximity of the majestic Jungfrau massive. The well equipped Congress Center of Interlaken will be the place of the Conference activities. The Conference activities will start in the evening of Monday, June 7, 1993, and proceed until Friday noon, June 11, 1993. Language The official language of the Conference will be English. No facilities for translation or interpretation will be available. Accommodation and Social Events Interlaken, a traditional alpine health resort, offers a choice of accommodation at various tariffs. A half-day Excursion and a Conference dinner are planned, as well as a programme for accompanying persons. Official carrier: Swissair You are recommended to check with Swissair or your local travel agent for the best flight arrangements for this period. Swissair offices round the world will assist you with your travel arrangements. Further Information If you did not receive the second circular, which was sent out early February, 1993, please contact the conference secretariat at the address given below. The second circular includes registration, abstract and hotel reservation form. 12th Annual Conference of the MGS P.O. Box 6, Clarastrasse 57 CH-4005 Basel, Switzerland Tel. ++41-61-691 51 11, Fax. ++41-61 691 81 89 +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From DAVID@UCONNVM.bitnet Wed Feb 10 05:46:29 1993 Message-Id: <199302101547.AA19594@oscsunb.ccl.net> Date: Wed, 10 Feb 93 10:46:29 EST From: carl david Subject: help with a new alpha (DEC) computer To: chemistry@ccl.net We have recently begun computing on a DEC3000 400AXP Alpha system, doing mostly X-PLOR and polarization model computations. Being a Vax novice, I wonder if I can pose some questions to the general user community, hoping that even if specific answers aren't known, people know others who might help. 1) Is there a general listserv environment for the VAX community? I.e., something like info-mac and info-ibmpc? 2) Is there FORTRAN or C source code molecular display graphics available that will run in this environment? 3) Is there a library such as SIMTEL for software in this area? Thanks for any help you can give me. Sincerely, Carl David From bjerkese@kjemi.unit.no Wed Feb 10 17:55:05 1993 From: "Leif Haldor Bjerkeseth . Organisk Kjemi" Message-Id: <199302101555.AA05815@hitra.kjemi.unit.no> Subject: G90/92. Scaled Freq. Correct. for H and S. To: chemistry@ccl.net Date: Wed, 10 Feb 1993 16:55:05 +0100 (MET) You have to scale the frequencies you get from Gaussian by about 0.9. The enthalphy, entropy and ZPE among other thermodynamical properties calculated by Gaussian depend upon the frequencies. Does someone on this list know how you can compute the thermodynamical properties using scaled frequencies in Gaussian? Probably not possible? If so, has someone written a program to extract the frequencies from the outputfile or chk-file, correct for the scaling and then compute the thermodynamical properties? Or do I have to use Lotus 1-2-3 or Excel after looking up the litterature references for all the formulas. Leif Haldor -- Leif Haldor Bjerkeseth, Dept.Org.Chem., NTH, UNIT, N-7034 TRONDHEIM Phone: +47 7 59 39 67 // Prefered E-mail address: bjerkese@kjemi.unit.no Fax: +47 7 59 42 56 // From YUAN%UCCHEM@UCBEH.SAN.UC.EDU Wed Feb 10 07:03:59 1993 Date: 10 Feb 1993 12:03:59 -0500 (EST) From: Jie Yuan Subject: Biosym Mail Reflector or Newsgroup? To: CHEMISTRY@ccl.net Message-Id: <01GUK0USPCVM8WW2GW@UCBEH.SAN.UC.EDU> Hi everyone! Do you know the mail reflector address or the newsgroup name for users of Biosym packages? Thanks a lot for your help! Jie Yuan From scheiner@qm.c-chem.siu.edu Wed Feb 10 05:59:14 1993 Message-Id: <00133.2812191785.13144@qm.c-chem.siu.edu> Organization: Southern Illinois University at Carbondale To: chemistry@ccl.net (osu theo) From: scheiner@qm.c-chem.siu.edu (Steve Scheiner) Date: Wed, 10 Feb 1993 11:59:14 CST Subject: MWTCC Subject: MWTCC CONFERENCE ANNOUNCEMENT MIDWEST THEORETICAL CHEMISTRY CONFERENCE XXVI to be held at Southern Illinois University Carbondale, IL May 20-22, 1993. The Conference will open on Thursday evening with a reception. Friday morning and afternoon will be devoted to contributed talks and posters, followed by a banquet in the evening. Talks and posters will continue on Saturday morning, with the Conference concluding at approximately noon. The Conference will be held in the informal environment of the University's Touch of Nature facility on the wooded shores of Little Grassy Lake, about 5 miles south of campus. This facility includes inexpensive hotel and cabin lodging in rustic surroundings. The MWTCC particularly encourages participation of students and provides a nurturing professional atmosphere for the first presentation of their work. Carbondale is located near the southern tip of Illinois. The Carbondale Amtrak stop lies directly along the line between Chicago and New Orleans. Airline access is through Marion, IL, which may be reached via a commuter airline through St. Louis. If you wish to receive mailings concerning this Conference, please respond to: Conference Organizer: Steve Scheiner Department of Chemistry Southern Illinois University Carbondale, IL 62901 steve_scheiner@qm.c-chem.siu.edu or ga0874@siucvmb.Bitnet ----- Steve Scheiner, Professor ga0874@siucvmb.Bitnet or steve_scheiner@qm.c-chem.siu.edu Dept. of Chemistry & Biochemistry Southern Illinois University at Carbondale ph: 618/453-6476 fax: 618/453-6408 From topper@haydn.chm.uri.edu Wed Feb 10 09:22:46 1993 Date: Wed, 10 Feb 93 14:22:46 -0500 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9302101922.AA05198@haydn.chm.uri.edu> To: bjerkese@kjemi.unit.no, chemistry@ccl.net Subject: Re: G90/92. Scaled Freq. Correct. for H and S. >You have to scale the frequencies you get from Gaussian by about 0.9. >The enthalphy, entropy and ZPE among other thermodynamical properties >calculated by Gaussian depend upon the frequencies. Does someone on this >list know how you can compute the thermodynamical properties using scaled >frequencies in Gaussian? Probably not possible? If so, has someone written >a program to extract the frequencies from the outputfile or chk-file, >correct for the scaling and then compute the thermodynamical properties? >Or do I have to use Lotus 1-2-3 or Excel after looking up the litterature >references for all the formulas. >Leif Haldor Dear Leif, You can certainly estimate thermochemical properties from the frequencies you get from Gaussian. However, you will have to use the rigid-rotator/ harmonic oscillator (RRHO) approximation to the partition function, which requires the three principal moments of inertia as well as the harmonic frequencies. These can be calculated from the molecular geometry and masses. Also, the calculation may only be semi-quantitative, unless you have a fancy way of estimating the partition function. My coworkers and I have recently written a paper on the calculation of thermochemical properties from potential energy surfaces using various methods, and the article will appear soon in the Journal of Chemical Physics (March 15 is the approximate date). In that paper, we compare the RRHO approximation of the free energy to calculations made using perturbation theory to treat the vibrations and to (exact) Fourier path-integral quantum Monte Carlo calculations for potential energy models of gas-phase H2O, D2O, H2S, and H2Se. However, we did not use "scaled" frequencies; we used the actual normal- mode harmonic oscillator frequencies. These resulted in partition functions which were off by as much as 30% from "exact" values (looking at temperatures between 200 and 4000 K). There's no telling whether using scaled frequencies would make the partition functions more accurate or less accurate, at least not >from first principles. I would be glad to send you a preprint of our work if you are interested (this is the same article that many people on the list have asked for in the context of coordinate transformations). Also, Martin, Francois and Gijbels have recently calculated thermochemical properties for H2O using Gaussian. A good reference is: Martin, Francois, and Gijbels, J. Chem. Phys. 96, 7633 (1992) Our work indicates that their calculations (which use vibrational perturbation theory in combination with a quantum non-rigid rotator calculation) are quite accurate up to 2400K. However, for molecules which can undergo internal rotations at the temperature of interest, all bets are off! Also, beware of very low-frequency (floppy) vibrations. A very useful approximate "harmonic" form for the vibrational partition function (if you know the zero-point energy and the fundamentals) is given in D.G. Truhlar and A.D. Isaacson, J. Chem. Phys. 94, 357 (1991) and you may also want to look at the JANAF tables; M.W. Chase Jr. et.al., JANAF Thermochemical Tables, 3rd ed. (ACS and APS for the National Bureau of Standards, New York, 1985). -Hope this helps! robert ******************************** * Robert Q. Topper, Ph.D. * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * rtopper@chm.uri.edu OR * * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** From feng@lisboa.ks.uiuc.edu Wed Feb 10 10:23:41 1993 From: Zhou Feng Message-Id: <9302102224.AA14244@lisboa.ks.uiuc.edu> Date: Wed, 10 Feb 93 16:23:41 -0600 To: CHEMISTRY@ccl.net Subject: parallel CHARMM? I heard that the CHARMM will be running in parallel on CM-5 soon. I would like to know more details, such as the performance and when is it going to be available. Any ideas? Feng phone 217-244-3667 email feng@lisboa.ks.uiuc.edu From rickl@iris118.biosym.com Wed Feb 10 07:46:43 1993 Date: Wed, 10 Feb 93 15:46:43 -0800 From: rickl@biosym.com Message-Id: <9302102346.AA23962@iris118.biosym.com> To: chemistry@ccl.net Subject: DIBUG addresses Jie Yuan asked for the name of a mail exploder for users of Biosym software. The group is called DIBUG (Discover Insight Biosym Users Group), and the email addresses are: dibug-REQUEST@comp.bioz.unibas.ch ... to subscribe/unsubscribe dibug@comp.bioz.unibas.ch ... to post messages dibug-ADMIN@comp.bioz.unibas.ch ... to talk to the administrator, Reinhard Doelz at the Biocenter of the University of Basel. Specific questions by customers about the software can be sent to: rcenter@biosym.com Richard H. Lee, Ph.D. Manager, Homology Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121-2777 USA From ilya@lisboa.ks.uiuc.edu Wed Feb 10 13:04:24 1993 From: Ilya Logunov Message-Id: <9302110109.AA14962@lisboa.ks.uiuc.edu> Date: Wed, 10 Feb 93 19:04:24 -0600 To: CHEMISTRY@ccl.net Subject: ZINDO program I would like to get the quantum chemistry program ZINDO for the spectra calculations. I intend to run it on SGI, NEXT, or Cray platform. Does anybody know how I can get it? Any response will be very much appreciated. Ilya Logunov From KUTZENCOP@st.cyanamid.com Wed Feb 10 15:08:08 1993 Date: Wed, 10 Feb 1993 20:08:08 -0500 (EST) From: KUTZENCOP@st.cyanamid.com (Philip Kutzenco) Message-Id: <930210200808.22413db7@st.cyanamid.com> Subject: RE: Biosym Mail Reflector or Newsgroup? To: CHEMISTRY@ccl.net Jie Yuan asks: >Do you know the mail reflector address or the newsgroup name for users of >Biosym packages? Send email to dibug-request@comp.bioz.unibas.ch to join the mail reflector for DIBUG ("Discovery, Insight, Biosym Users' Group"). DIBUG bills itself as "an unmoderated mailing list for discussion of Biosym products. Expected topics of discussion include, but are not limited to, queries about how to use features of the software, and how to solve scientific problems using the software. Although this list is administered by and for Biosym users, we expect Biosym Technologies, Inc. to monitor the list, and perhaps to respond to issues that may arise." Phil Kutzenco kutzenco@cyanamid.com From mail Wed Feb 10 11:19:49 1993 From: hyper!burton (Ian Burton) Message-Id: <9302101542.AA28995@hyper.hyper.com> Subject: Re: parallel workstations and servers To: chemistry@ccl.net Date: Wed, 10 Feb 1993 10:42:43 -0500 > >Are any of the software vendors taking advantage of the new machines that >Sun, SGI, Kubota and others are marketing? In other words, is commercial >software running in parallel? Replies from Biosym, MSI, Gaussian and >others are solicited and welcome. > >Doug > >Douglas A. Smith >Assistant Professor of Chemistry >The University of Toledo >Toledo, OH 43606-3390 > >voice 419-537-2116 >fax 419-537-4033 >email dsmith@uoft02.utoledo.edu > > >--- >Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator >OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net >CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first >--- > Dr. Smith, HyperChem already does. In response to your inquiry, the SGI Workstation release of HyperChem already does take advantage of multiple processors. In this release, there is a Communications... option in the Setup menu, which allows the user to specify the number of nodes which the computation will be distributed over, as well as specify whether the computation will be performed on the local or a remote host. After the number of nodes is specified, the kernel then is responsible for distributing these over multiple processors. If the number of nodes exceeds the number of processors, then the kernel may emulate multiple processes, but these will not be running in parallel. This should not change for the new SGI series of workstations. In release 2.0 of the SGI Workstation version of HyperChem Extended Huckel, CNDO, INDO, MINDO/3, MNDO, AM1, PM3, AMBER, BIO+ and OPLS all have the ability to run on parallel processors. Cheers, Ian. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2