From lhuber@ncsa.uiuc.edu Tue Oct 27 04:35:47 1992 Date: Tue, 27 Oct 92 10:35:47 -0600 To: chemistry@ccl.net From: lhuber@ncsa.uiuc.edu (Lee Huber) Subject: AMBER and XLEAP Info? Please send me information about graphical interfaces to AMBER and names to contact for information. My understanding is that there is a program called "XLEAP" which is such an interface. Does anyone have info about this program? Thanks in advance for your help. Lee Huber ---------------------------------------------------------------------- Lee M. Huber e-mail: lhuber@ncsa.uiuc.edu Dow Chemical Company/NCSA voice: 217-244-4697 605 East Springfield Ave., 128CAB fax: 217-244-4694 Champaign, IL 61820 ---------------------------------------------------------------------- From taaffe@siam.org Tue Oct 27 06:58:58 1992 Date: Tue, 27 Oct 92 11:58:58 EST From: STT To: chemistry@ccl.net Subject: SIAM Conference on Simulation... SIAM Conference on Simulation and Monte Carlo Methods August 4-6, 1993 Cathedral Hill Hotel San Francisco, California Invited Presentations Monte Carlo Methods Using Quasi-Random Sequences Russel Caflisch Trade-off Between Path Length t and Number of Paths n When Starting in Steady State; George S. Fishman Gradient Estimation in Discrete-Event Simulations Paul Glasserman Derandomizing Algorithms Michael Luby Evolution and Ecology of Digital Organisms Thomas Ray Evolutionary Algorithms Versus Mathematical Programming Techniques; Hans-Paul Schwefel Aspects of Markov Chain Monte Carlo in Bayesian Statistical Calculations; Adrian Smith Computer Simulation of Biological Molecules Robert H. Swendsen Error Analysis of Stochastic Algorithms for Nonlinear Partial Differential Equations; Denis Talay Deadline for Abstract Submission: January 22, 1993. Deadline for minisymposium proposal submission: December 21, 1992. Information on how to contribute, as well as additional program and registration materials available by contacting: SIAM - Society for Industrial and Applied Mathematics 3600 University City Science Center Philadelphia, PA 19104-2688 U.S.A. Telephone: 215-382-9800; Fax: 215-386-7999 E-Mail: meetings@siam.org Science and Industry Advance With Mathematics From wsonnen@alnitak.usc.edu Tue Oct 27 03:23:16 1992 Date: Tue, 27 Oct 92 11:23:16 PST From: wsonnen@alnitak.usc.edu (Wayne Sonnen) To: chemistry@ccl.net Subject: reproducibility on SGI Dear netters, We have a problem with reproducibility on a SGI machine. We seem to get different results of two identical calculations (i.e. exactly the same starting configurations, etc.). The results initially are within the precision of the machine, but begin to diverge from one another and this divergence continues to grow. Has anyone had similar experiences with SGI machines? Any suggestions (eg. recompling) on "fixing" this problem? your comments are appreciated. Thank you, Wayne Sonnen wsonnen@alnitak.usc.edu From lhuber@ncsa.uiuc.edu Tue Oct 27 10:40:40 1992 Date: Tue, 27 Oct 92 16:40:40 -0600 To: chemistry@ccl.net From: lhuber@ncsa.uiuc.edu (Lee Huber) Subject: re: AMBER and XLEAP Info? The replies to my recent request are attached. The rapid response was appreciated. Lee Huber > >Please send me information about graphical interfaces to AMBER and names to >contact for information. My understanding is that there is a program >called "XLEAP" which is such an interface. Does anyone have info about >this program? > >Thanks in advance for your help. >Lee Huber >---------------------------------------------------------------------- >Lee M. Huber e-mail: lhuber@ncsa.uiuc.edu >Dow Chemical Company/NCSA voice: 217-244-4697 >605 East Springfield Ave., 128CAB fax: 217-244-4694 >Champaign, IL 61820 >---------------------------------------------------------------------- > Shankar Subramaniam (U. of IL.) said that both Insight II(Biosym) and Macromodel can use an AMBER format. ================== >Date: Tue, 27 Oct 92 13:25:32 -0800 >From: howard@cgl.ucsf.edu (Allison Howard) >To: lhuber@ncsa.uiuc.edu >Subject: LEaP > > >Dr. Huber, > >Hello. I just saw your message on the OSC mailing list. I am a member >of the Kollman group at UCSF. > >Regarding LEaP: >1) LEaP is a program that allows one to prepare molecules to programs >such as AMBER and SPASMS. >2) There are actually two LEaP programs: a) tLEaP-a non-graphical version >and b) xLEaP- a graphical version. >3) The program was written by Chris Schafmeister of Peter Kollman's lab. >4) The beta version of the program will be sent out around 1 December >1992. >5) LEaP is actually much more than a front-end. We think of it as >a workbench for computational chemistry. When it is completely >finished, a user will be able to prepare molecules, generate input >files for several programs (the first are AMBER, SPASMS, and the >Kuntz program DOCK), develop parameters for molecular mechanics, >start runs of th above mentioned programs, and gather output from >these programs. >6) The LEaP program that will be sent to users will consist of >code (K&R C) and documentation. The graphics manipulations are >done in X-windows. > > >I will keep your address so we can send you mail when the release >is imminent. If you have any specific questions about LEaP, I >would be happy to answer them. You might also want to send mail >to >Peter Kollman >Dept of Pharmaceutical Chemistry >UCSF >San Franciso CA 94143 > > >Allison Howard >howard@cgl.ucsf.edu ========================= >Date: Tue, 27 Oct 92 13:27:11 -0800 >From: ross@cgl.ucsf.edu (Bill Ross) >To: lhuber@ncsa.uiuc.edu >Subject: Re: AMBER and XLEAP Info? > >In case no one else has replied, davidr@cgl.ucsf.edu is the one to ask. >Also, let me know if you want info about the amber reflector or the 4.0 >release. I can also send license agreement etc. > >Bill Ross > From CHFW@cc.newcastle.edu.au Sun Oct 28 20:53:50 1992 Date: 28 Oct 1992 09:53:50 +1100 From: CHFW@cc.newcastle.edu.au Subject: MM2 AND MM3 To: chemistry@ccl.net Dear Netters: A friend of mine is going to start her master degree soon. Part of her work is to do some calculations on some crystal structure by MM2 or MM3(Molecular Mechanics). She will be apreciated to listen to some comments about MM2 and MM3 made by computational chemistist. Does anyone know well about the MM's? Thanks in advance. Feng WANG -- | Feng WANG Department of Chemistry, The University of Newcastle | | Callaghan, N.S.W.2308, Australia | | Internet: chfw@cc.newcastle.edu.au Tel: +61 49 215 475 | |______________________________________________________________________________ From cramer@chemsun.chem.umn.edu Sat Oct 27 14:55:49 1992 Date: 27 Oct 1992 20:55:49 -0600 (CST) From: Christopher Cramer Subject: AMSOL for Cray Y-MP To: chemistry@ccl.net Regarding Kevin Moore's query for an AMSOL version portable to the Y-MP, the version currently distributed by QCPE (3.0.1) was tested on the San Diego Y-MP and found to perform satisfactorily. QCPE has cataloged AMSOL 3.0.1 as program 606. The following details on portability are included, as appearing in the QCPE Bulletin: AMSOL-version 3.0.1 is written in FORTRAN 77 with the INCLUDE extension. It has been tested on Cray-2, Cray X-MP-EA, and Cray Y-MP computers with the UNICOS 6.1 and 6.1.5a versions of Unix and the cft77 compiler, on an IBM RS/6000 workstation with the AIX Unix operating system version 3.1.5, on a Sun SparcStation 4/330 with the SunOS operating system 4.0.3, and on an IRIS 4D workstation with the IRIX Unix operating system version 4.0.1. It is distributed as a set of 108 files, including C shell scripts for compiling and linking, for interactive job submission, and for submitting batch jobs under the NQS queuing system. The distribution also includes a brief on-line manual (ASCII documentation file), which assumes that the user is familiar with AMPAC, a 40-run test suite, and a set of subroutines with Cray library calls which may be used to make a partially optimized Cray version, called version 3.0.1c. AMSOL-versions 3.0.1 and 3.0.1c are unlicensed. -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431