From laaksone@csc.fi Fri Mar 26 05:08:44 1993
Date: Fri, 26 Mar 1993 07:08:44 -0200 (EET)
From: Leif Laaksonen <Leif.Laaksonen@csc.fi>
Subject: Re: amber/insight
To: Bill Ross <ross@cgl.ucsf.edu>
Message-Id: <Pine.3.05.9303260742.A28631-b100000@convex.csc.fi>
On Thu, 25 Mar 1993, Bill Ross wrote:
> For those who want to display Amber trajectories, there are two
> programs I know of in QCPE that do this:
>
> MD Display by Terry Lybrand and coworkers [SGI only]
> mdXvu by Mark Forster [xwindows in general]
>
> Also, for people who want to import Amber output files to other
> programs we (distributor of Amber) will supply a routine to read
> the "parm" file that defines identity and connectivity of the atoms
> in coordinate dumps.
>
> Bill Ross
There is also the SCARECROW program which can show trajectories
from CHARMM, DISCOVER, YASP, MUMOD and AMBER. Currently
SCARECROW works only on SGI boxes but I'm slowly working on
a Motif port.
-leif laaksonen
-------------------------------------------------------------------
Leif Laaksonen |
Center for Scientific Computing | Phone: 358 0 4572378
P.O. Box 405 | Telefax: 358 0 4572302
FIN-02101 Espoo | Voice Mail: 358 486257407
FINLAND | Mail: Leif.Laaksonen@csc.fi
One of these days
I'm going to sit down and write a long letter
To all the good friends I've known
One of these days by Neil Young
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From radomski@mond1.ccrc.uga.edu Fri Mar 26 04:11:49 1993
Message-Id: <9303261411.AA29223@mond1.ccrc.uga.edu>
To: chemistry@ccl.net
Subject: Neural Networks in Spectroscopy
Date: Fri, 26 Mar 93 09:11:49 -0500
From: radomski@mond1.ccrc.uga.edu
Hi Netters,
for all of you who while attending next week ACS meeting in
Denver are going to drop by the DEC's booth to see their
newest line of alpha workstations I've the following.
If you are interested in applications of neural nets to spectro-
scopy try to be there when Jan Thomsen of CCRC would be
giving a demonstration of his program - ANCHOVY (on DEC's
alpha). To my best knowledge this is first time ever when
neural nets are effectively used for a very quick database
searches.
Unfortunately, I won't be present. However, as most of the
examples, spectra, network architectures, their training and
so on, which Jan will be using to demo his program, are taken
directly from my ongoing projects - I'd be very curious and
glad to hear all your comments and opinions. Please write to
me direct or use the list, whatever you prefer.
Jan Radomski
Complex Carbohydrate Research Center,
University of Georgia,
Athens, US.
From 100012.1163@compuserve.com Fri Mar 26 09:47:52 1993
Date: 26 Mar 93 14:47:52 EST
From: "100012.1163@compuserve.com" <100012.1163@compuserve.com>
To: <CHEMISTRY@ccl.net>
Subject: Molecular Modelling on a PC
Message-Id: <930326194752_100012.1163_BHB35-3@CompuServe.COM>
To: >internet:CHEMISTRY@oscsunb.ccl.net
Dear Fellow Netters, Molecular Modelers and Computational
Chemists,
The molecular modelling program MOBY 1.5 is now ready for
shipping. A *free* demonstration version is available.
MOBY VIA ANONYMOUS FTP
The demonstration version of MOBY, version 1.5 may be obtained
via anonymous FTP from benny.bsc.mass.edu (or 134.241.41.5). If
you have access to a computer on the Internet which supports
FTP (file transfer protocol), log on to the computer and use
the following sequence of commands (use lower case throughout):
ftp benny-bsc.mass.edu <cr>
anonymous <cr>
your-email-address <cr>
cd pub <cr>
cd moby <cr>
binary <cr>
get mobyread.me <cr>
get mobydemo.exe <cr>
get manualps.exe <cr>
quit <cr>
At this point you will have the binary version of the files in
your directory on the computer that is connected to the
Internet. Your local information Services folk can advise you
on the best way to transfer these files to your microcomputer.
MOBY version 1.5 runs best on a 486 or 386. The 386 will
require a math coprocessor. If you have a problem with the
local file transfer, it will probably be that the files are not
being transferred as binary files.
mobydemo.exe is a self-extracting archive file that contains
the demo version. manualps.exe is a self-extracting file that
contains a postscript version of the demo manual. Make a
directory called MOBY and copy the files to it. Theo run the
files and they will self-extract. If you have Problems with
this process, you can email to CHIPMAN@TOPCAT.bsc.mass.edu
MOBY VIA E-MAIL
The demonstration version of MOBY, version 1.5 may be obtained
via e-mail from InterNet:SVSERV@DHDSPRI6.BITNET. To receive the
files, send the following commands in the body of your message:
get /chemistry/mobydemo.exe
get /chemistry/manualps.exe
MANUALPS.EXE is a self-extracting archive with the manual for
the demo in encapsulated postscript format (the printing area
is A5, so it should print on letter or legal format paper).
If you encounter problems, please send a message to:
stumpe@spint.compuserve.com
Dr. Chipman has kindly advised Springer-Verlag in improving the
English language version of MOBY 1.5. He has extensively tested
MOBY in classes and he has agreed to answer any questions you
may have.
USING MOBY WITH OTHER PROGRAMS
Version 1.5 of MOBY can be used as a "front end" to draw
structures for input into other programs, such as MOPAC. MOBY
can output a structure that can be used directly in MOPAC. This
file format, called a Z-matrix, can be used by many molecular
modeling and quantum mechanics programs. MOBY will also save
structures in the form of molfiles for use in the MACCS-II data
base. Molefiles contain the structure in the form of cartesian
coordinates and can be used by many other programs.
MOBY will also read MOPAC output files, either from MOPAC or
from the many other programs which write MOPAC output files.
All you have to know to use a MOPAC file with MOBY is that the
first three lines of the file are reserved for information
about the MOPAC calculation (keywords) and the name of the
molecule. When you read a MOPAC file into MOBY, MOBY prompts
you for the number (3) of lines to be skipped. Therefore, MOBY
can be used to visualize structures resulting from the MOPAC
calculation directly.
A software routine QC4MOBY is available to MOBY users to
extract geometry, IR- and UV spectral data and molecular
orbital data from files generated with the Quantum Chemistry
programs MOPAC 6.0, SCAMP 4.2 or GAUSSIAN 82/90. The converted
files can be read by MOBY version 1.5.
MOBY offers an extensive range of modelling functions:
- Display of up to 2000 centers
- Fast 3D graphics
- Independent manipulation of freely-definable
fragments
- Structure comparison
- Property comparison
- Force field calculations on up to 150 centers
interacting with up to 2000 other centers
- Geometry optimization
- Conformational analysis
- Molecular dynamics simulation
- Extensive tools for the energy analysis of
structures
- Quantum chemical calculations based on the
semi-empirical MNDO and AM1 methods
- Display of:
- IR spectra and normal coordinates
- UV/Visible spectra
- Molecular orbitals
- Isopotential surfaces for electrostatic potentials
- Freely-definable format for reading non-MOBY
geometry data
- Library of important structures and their
geometries
- Construction and maintenance of an individual
structure
library
- On-line help
- PROTOCOL mode for recording a program session
- DEMO mode for re-running a previously recorded
program session
This latest version, MOBY 1.5, is for IBM-PC-compatible
personal computers with the following minimum specifications:
- 640 kb random access memory (530 kb free)
- 80x87 arithmetic coprocessor
- graphics adapter: Hercules, EGA, or VGA (1024x768
maximum)
- a mouse and
- a hard disk are strongly recommended
running under MS-DOS version 2.0 or later.
Since MOBY requires 530 kB of random access memory to be free,
MS-DOS Version 4.0 is not a good choice; MS-DOS 5.0 is strongly
preferred.
MOBY 1.5 will be demonstrated at the Spring ACS Meeting. Look
for the Springer-Verlag booth. For more information write to:
In North America:
Springer-Verlag New York
Electronic Media Services
c/o Ms. Raye Hazan
175, Fifth Avenue
New York, NY 10010
USA
Phone: (212) 460-1653
Fax: (212) 473-6272
InterNet: Hazan@SPINT.CompuServe.com
Sincerely yours
Dr. Rainer Stumpe
Chemistry Editorial
Springer-Verlag
Tiergartenstr. 17
D(W)-6900 Heidelberg
Phone: +49-(0)6221-48 73 10
Fax: +49-(0)6221-41 39 82
INTERNET:stumpe@spint.compuserve.com