From chemistry-request@ccl.net Sat Mar 16 01:10:41 1991 Date: Sat, 16 Mar 91 00:56 EDT From: DMITRIENKO@GIDWAT.UWaterloo.CA Subject: software for the AMIGA 3000UX ? To: chemistry@ccl.net Status: R Our Faculty of Science has received a "gift" of a number of Amiga 3000UX workstations running UNIX SVR4. I would like to put them to good use as research/teaching tools for chemistry and biochemistry and hence would appreciate any information concerning computational chemistry and molecular modelling software which is known to be compatible with this system. Any advice will be appreciated. Regards, Gary Dmitrienko Department of Chemistry University of Waterloo Waterloo, Ontario, Canada N2L 3G1 (519)-888-4642 --- From chemistry-request@ccl.net Sat Mar 16 16:25:15 1991 Date: Sat, 16 Mar 1991 14:56:59 CST From: jgolab@ncsa.uiuc.EDU Subject: Brookhaven Files To: CHEMISTRY@ccl.net Status: R Recently, a few messages have appeared on this bulletin board about the Brookhaven Protein Data Bank (BPDB). The BPDB contains the three-dimensional atomic coordinates of several hundred proteins, nucleic acids, and polysaccharides as well as some VAX/VMS FORTRAN programs. Currently, the BPDB is a compendium of over seven hundred ASCII files that is updated every three months at BNL. In October 1989, the National Center for Supercomputing Applications (NCSA) became a member of the Protein Data Bank Service Association (PDBSA) sponsored by Brookhaven National Laboratory (BNL). NCSA is one of four national supercomputer centers funded in part by the National Science Foundation and is located on the Urbana-Champaign campus of the University of Illinois. As a member of the PDBSA, NCSA is one of ten centers around the world that can provide online distribution of the Brookhaven Protein Data Bank (_legally_). To the best of our knowledge, the BPDB files are not electronically available through any other means, e.g. via anonymous ftp protocol, except through one of these centers. People who access the Brookhaven Protein Data Bank files at NCSA are required to fill out and sign an Advisory Notice form in keeping with the distribution agreement between NCSA and BNL. As a result of this requirement, the ASCII files of the BPDB are password protected on the NCSA Cray systems. Once your completed Advisory Notice is received at NCSA, this password (and its quarterly update) will be sent to you until you inform NCSA that you no longer require this service. For those of you who do not have an NCSA Cray account, a restricted shell login has been set up that allows access to and ftp transfer of the BPDB files to your site. To obtain a copy of the Advisory Notice, send your complete name and address to Dr. Joe Golab via electronic mail at jgolab@ncsa.uiuc.edu (Internet) or u12688@ncsagate (BITNET) or by phone at (217) 244-2756. Within a couple of weeks, you will be able to access the BPDB files at NCSA as often as you wish. The Brookhaven Protein Data Bank Newsletter can be obtained by sending your name and address to: Ms. Frances C. Bernstein/ Protein Data Bank/ Chemistry Department/ Brookhaven National Laboratory/ Upton, New York 11973/ USA. You should note that filling out the Advisory Notice at NCSA automatically places your name on the newsletter mailing list. :Joe Golab @ NCSA - University of Illinois --- From chemistry-request@ccl.net Sat Mar 16 19:08:42 1991 Date: Sat, 16 Mar 91 18:58:06 From: D342NS1B@VB.CC.CMU.EDU Subject: molecular conformations To: chemistry@ccl.net Status: R I have recently become interested in the problem of predicting molecular conformations. I would appreciate it if someone could give answers or point to appropriate references addressing the following questions: 1) Why is predicting molecular conformations important? What are the most important applications where we need to be able to predict molecular conformations? 2) What are the most popular methods used? 3) Is it true that all curently known methods for finding the minimizers of the potential energy function suffer from the existence of multiple local minima? ie. they provide no guarantee for finding the conformations corresponding to the global min of the energy surface? 4) If the answer to question (3) is yes, then: Is it important that we be able to find global minima and what are we missing when we make use of currently available packages/approaches? Thank you in advance. Dr. Nikolaos Sahinidis Department of Chemical Engineering Carnegie Mellon University ARPAnet: d342ns1b@VB.CC.CMU.EDU BITNET: d342ns1b@CMCCVB ---