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

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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

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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

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