|
|
| From: |
fredvc : at : esvax.dnet.dupont.COM |
| Date: |
Mon, 13 Apr 92 10:06:49 -0400 |
| Subject: |
PC-BASED MOLECULAR MODELING PACKAGES |
Netters:
First, let me thank all of you that responded to my query regarding
PC-based software for molecular modeling. Based on these responses, the most
widely used packages at present are ALCHEMY from Tripos, and PCMODEL from
Serena. Interestingly, the next most frequently mentioned package (HYPERCHEM
from Autodesk) has just been released, and there really hasn't been time for
development of anecdotal information.
I have organized the material first by product, with user information
separated from vendor information, if any. (ALCHEMY, PCMODEL, & HYPERCHEM are
listed first, with the rest in alphabetical order.) Next, pointers to reviews
are included, followed by any "general information" at the end. I hope that
this compendium is useful.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
FREDERIC A. VAN-CATLEDGE
Scientific Computing Division || Office: (302) 695-1187
Central Research & Development Dept. || FAX: (302) 695-9658
The Du Pont company ||
P. O. Box 80320 || Internet: fredvc { *at * }
esvax.dnet.dupont.com
Wiilmington DE 19880-0320 ||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*************************************************************************
ALCHEMY III - User Info
-------------------------------------------------------------------------
Alchemy III is a fragment model builder using a modified Sybyl or MM3 force
field to do molecular mechanics.
--
>>"GERSON "at@at" DFWVM04.VNET.IBM.COM" "Dr. Dennis Gerson"
ALCHEMY is a junior version of SYBYL and has a lot of good capabilities. It
runs on both MACs and IBMs. ALCHEMY (above) is the one with the tie to
Chemical Abstracts.
This means results of 3D searching can be viewed in ALCHEMY.
--
>>"MARTIN;at;cmda.abbott.com" "MARTIN%CMDA"
I strongly suggest that you look into ALCHEMY which is distributed by Tripos
(1-800-323-2960). It's really good and really cheap.
--
>>"PEARLMAN "-at-" VAX.PHR.UTEXAS.EDU"
There's the Alchemy II package from Tripos, which runs on PC's and MAC's,
which have structure building/visualization, and some energy minimzation
for structure refinement. Energy minimizations are not terribly
sophisticated, but do provide a relatively inexpensive entry into the
modelling world.
--
>>Steven W. Layten/Chemical Abstracts Service/ PO Box 3012, Columbus, OH 43210
>>INET: swl26.,at,.cas.org BITNET: swl26.,at,.cas UUCP:
osu-cis!chemabs!swl26
>># # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # #
Alchemy from Tripos Assoc.s is slightly more complicated (re: PCMODEL), but
also more sophisticated. I have only used Alchemy as a loaner
from Tripos during a computational chemistry workshop for under-
graduate professors run by Roger DeKock (deko -x- at -x- calvin.edu).
--
>>Michael A. Peterson/Indiana Univ.-Purdue Univ. $#at#$ Indianapolis
>>ipmp500 - at - indyvax.iupui.edu
Alchemy-III Tripos
Nice graphics, simple structure building and MM,
fitting, interactive torsion adjustment, etc. Nicely
done. Uses bizarre Tripos file format that's difficult
to convert to/from anything else.
(MAC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb { *at * } uunet.UU.NET
Tripos has Alchemy 3 for PCs - We have used verison 2. and it works for small
(20-50) atom systems. As for anecdotal information, I have been teaching
modeling at R&H for 10 years now, and I usually hook 1 or 2 scientists each
year. Recently Tripos Alchemy was the prefferred PC solution, but at the ACS
meeting I will reevaluate them again.
--
>>Thomas Pierce,
>>tpierce-: at :-rohmhaas.com or rs0thp-: at :-rohvm1
>> Official Disclaimer:"The opinions expressed are those of the writer
>> and not the Rohm and Haas Company."
We use two pc-based modelling programs:
Alchemy II from Tripos has superior (re: PCMODEL) 3-D drawing and viewing tools
--
>>"defrees-: at :-almaden.ibm.com"
-------------------------------------------------------------------------
ALCHEMY III - Vendor Info
-------------------------------------------------------------------------
Here at TRIPOS we offer a program for the PC called ALCHEMY. This month we
are releasing the latest version, ALCHEMY III. You have a choice of a DOS
or Windows version (or Macintosh version). The commercial price is
$950. One tremendous advantage of this package is the ability to transfer
files to high end programs like SYBYL and LabVision for further analysis.
I am sending you information. If you wish to call, feel free to do so.
--
>>Michael Sullivan/TRIPOS Assoicates/(314) 647-1099/(314) 647-9241 (FAX)
>>email: tripos!krypton!mike "-at-" uunet.UU.NET
----------------------------------------------------------------------------
****************************************************************************
PCMODEL - User Info
----------------------------------------------------------------------------
PCMODEL is a "line drawing" builder using a modified MMX or Macromodel Force
field to do molecular mechanics. It also has simple solvent dynamics and
a limited version of conformation searching. It requires 386/387 or higher
cpus to work well.
--
>>"GERSON #*at*# DFWVM04.VNET.IBM.COM" "Dr. Dennis Gerson"
Try PCModel - Serena Software, Bloomington, Indiana.
Many features workes well with 150-250 atoms. Use it all of the
time on my Mac. It runs on both the Mac and PC.
--
>>"FAX0157 at.at uoft02.utoledo.edu" "JGANO at.at UOFT02 or 537-2104"
I have used PCModel by S[Cerena Software, Box 3076, Bloomington, IN 47420-3076
(Ph 812-333-0823) for some time now and I find it very easy to use. You need a
math coprocessor, mouse, and 550K of free ram to run. There are versions for
other platforms also.
--
>>Jim Macmillan/Department of Chemistry/University of Northern Iowa
>>MACMILLAN()at()ISCSVAX.UNI.EDU
Serena Software has PCMODEL available for DOS PC, Mac II, and
some workstations as well. This is a molecular modeling program
that has nice looking graphics and is easy to use. It supports
a wide range of input file formats to read from and write to,
including MM2, MNDO, MOPAC, Sybyl, Macromodel,Chem-3D and Alchemy.
--
>>Michael A. Peterson/Indiana Univ.-Purdue Univ. .,at,. Indianapolis
>>ipmp500 $#at#$ indyvax.iupui.edu
PCmodel Serena Software
This program has been available for several years and
seems to have a good reputation; I think its primarily
a PC-version of MM2 and some semi-empirical programs,
plus a graphics interface.
(PC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb-0at0-uunet.UU.NET
PCMODEL is useful too. I do not have an address. I recommend that you got to
the ACS Symp. in San Francisco. The exposition is bursting with PC
modeling packages. AutoCad is developing HyperCHem.>
--
>>Thomas Pierce,
>>tpierce &$at$& rohmhaas.com or rs0thp &$at$& rohvm1
>>Official Disclaimer:"The opinions expressed are those of the writer
>>and not the Rohm and Haas Company."
We use two pc-based modelling programs:
PCModel from Serena Software has superior (re: ALCHEMY II) modelling
capabilities
--
>>"defrees %! at !% almaden.ibm.com"
I have been using PC-Model for some time now and like it very much.
It is available from
Serena Software
P.O. Box 3076
Bloomington, IN 47402-3076
Phone: 812 885-9415
The last cost I heard was $250 for academic users, and I think it is about
double that for others. The program is easy to use and has a lot of features.
You should also get their MMX program to accompany it.
--
>>Jack Houser/Department of Chemistry/The University of Akron
>>"R1JJH%AKRONVM : at : VM1.CC.UAKRON.EDU"
----------------------------------------------------------------------------
PCMODEL - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
HYPERCHEM - User Info
----------------------------------------------------------------------------
By chance (a friend is applying for a position ...) I've heard that Autodesk
(most famous for their AutoCAD) is just now trying to enter the market with a
product called "Hyperchem" (or similar). I think my friend's got a copy to
try, but I didn't have the time yet ...
--
>>"sauer { *at * } igc.ethz.ch" "Wolfgang Sauer"
Check out HyperChem, which is just about to be released by Autodesk. I think
this product will have a significant impact on the community, although it
really requires something like a 486 machine to work well. I've seen
pretty detailed demos and it looks like a good product. Availability and
prices should be available by about the end of March from Autodesk.
--
>>david case
>>email: "case $#at#$ scripps.edu"
Can only suggest HyperChem from the folks at AutoDesk (creators of AutoCad).
Looks to be a good package - much more than a toy.
--
>>Kari Seger/University of Toledo/Department of Chemistry
>>email: grx0633 # - at - # uoft02.utoledo.edu
----------------------------------------------------------------------------
HYPERCHEM - Vendor Info (LOOOONNNGG!!!)
----------------------------------------------------------------------------
Autodesk, Inc will soon be shipping a new Windows-based molecular
modeling package called HyperChem. HyperChem runs on a 386/486 PC under
Microsoft Windows. It includes the capabilties to:
o Draw molecules in 2D and have a 3D structure automatically
generated by the built-in Model Builder
o Import files such as Brookhaven Protein Data Bank files and
then edit and modify them
o Create complex proteins and nucleic acids (DNA/RNA) using
built-in residue templates (custom residues can be added)
o Visualize structures in stick, sphere, dot surface, stereo and
other renderings
o Rotate, translate, Z-plane clip molecules, etc for better
visualization
o Calculate structural information such as bond angles, lengths,
torsion angles, interatomic distances, chirality, etc
o Label and display information such as atom type, charge,
residues/sequence, backbones, etc
o Put constraints on specific bond lengths, angles, torsions
o Do geometry optimization and single point energy calculations
using four different Molecular Mechanics force fields
o Calculate and plot electronic properties such as total charge
density, electrostatic charge density, spin density and
individual atomic orbitals using six different semi-empirical
quantum mechanical methods
o Do Molecular Mechanics or Semi-empirical quantum calculations
on selected areas of a structure
o Do Molecular Dynamics simulations using either Molecular
Mechanics or Semi-Empirical methods.
o Solvate molecules in a periodic box and then run any of the MM
or SEQM analyses on the system
o Customize and extend HyperChem through a built-in scripting
language by writing scripts to automate tasks and experiments,
interacting with other Windows programs such as Excel, or by
writing custom applications with programs such as Microsoft
Visual Basic that look and act like a built-in function of
HyperChem
Autodesk is located in Sausalito, CA and can be reached at 1-800-424-9737
--
>>email: autodesk!Joel_Voelz%3HARBOR "at@at" fernwood.mpk.ca.us"
------------------------------------------------------------------------------
I saw your note on the OSC chemistry e-mail group concerning molecular
modeling software on the PC. I work for Hypercube, and we are the
developers of Autodesk's HyperChem, which is just such a package.
HyperChem is to be released any day now: it just went to production
yesterday.
I won't be able to give you an outsider's view of HyperChem, of course,
but in brief what it does is the following:
(1) It runs under Microsoft Windows, and has capability to exchange
information with other applications (spreadsheets, wordprocessors, etc.),
via DDE and through the WIndows clipboard.
A Silicon Graphics version is due for release later this year.
(2) It contains a graphical front end that enables molecules to be
drawn easily (there is a model-building capability that produces 3D
structures from rough sketches). It has an extensive range of
facilities for manipulation and display of molecules. Proteins and DNA
fragments can be built residue-by-residue in a particularly easy manner.
(3) It contains four molecular mechanics force fields: MM+ (our
implementation of MM2, with a default scheme to fill in the gaps in
parameters), OPLS, AMBER and BIO+ (our implementation of the CHARMM
force field, including the published parameters).
(4) Using these force fields, geometry optimizations on all or part
of a system can be carried out, using constraints where needed.
(5) Using these force fields, molecular dynamics calculations can be
carried out, again on all or part of a system and with or without
constraints. There are playback tools for analysis of molecular
dynamics runs, and geometrical features as well as energies can be
monitored during a run.
(6) It contains our implementation of six semi-empirical methods.
Extended Huckel, CNDO, INDO, MINDO/3, MNDO and AM1. PM3 parameters are
available for the latter option. Geometry optimizations can be carried
out using these methods (except for Extended Huckel), and also molecular
dynamics (if you have the time to wait!). CNDO and INDO calculations
can also be carried out on part of a system, with the remainder serving
as an electrostatic background.
(7) All the molecular mechanics and semi-empirical parameters are
available in files, and can be added to and changed by the user.
(8) There is an extensive set of scripting (macro) commands, that
can be run as scripts from within the program or built into macros from
other Windows applications.
via DDE.
Should you require any other technical information, please
do feel free to contact me. Autodesk has a product information line at
1-800-424-9737, or you can FAX them at 1-415-491-8311.
--
>>Tom Slee/Hypercube, Inc.,/#7-419 Phillip St., Waterloo, Ont. N2L 3X2
slee ( ( at ) ) hyper.com
****************************************************************************
CACHE - User Info
----------------------------------------------------------------------------
do you know about Tektronic's CAChe (MacIntosh-based) product?
--
>>"cushing (+ at +) smoked.cse.ogi.edu" "Judy Bayard Cushing"
----------------------------------------------------------------------------
CACHE - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
CHEM3D - User Info
----------------------------------------------------------------------------
CHEMDRAW has CHEM3D or something like that for a name--Cambridge Scientific. It
has good capabilities for modeling with MM2, etc. They are also working on
simple database stuff.
--
>>"MARTIN -x- at -x- cmda.abbott.com" "MARTIN%CMDA"
----------------------------------------------------------------------------
CHEM3D - Vendor Info
----------------------------------------------------------------------------
We (Cambridge Scientific Computing, Inc.) produce a product called Chem3D
Plus for the macintosh which includes 3D model building and energy
minimization and molecular dynamics using the MM2 force field. In
combination with ChemDraw, you can draw structural formulas with
user-definable superatom names and do a 2->3D conversion. I will leave it
to others to review the packages, but if youUd like literature sent to you,
please let me know.
--
>>Stew Rubenstein, President/CSC, Inc.
>>email: sdr %-% at %-% mercury.camsci.com
****************************************************************************
CHEM-X - User Info
----------------------------------------------------------------------------
Chem-X Chemical Design
Presumably you already know about this - Joe
certainly should. I think they have a stand-alone
program in addition to the one that requires a
workstation host.
(MAC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb-: at :-uunet.UU.NET
----------------------------------------------------------------------------
CHEM-X - Vendor Info
----------------------------------------------------------------------------
CHEM-X is now available for IBM PC compatible
computers. We have not received a copy yet but believe it is almost
identical to the version that we are currently running on the VAX. The
contact number in the USA is:-
Chemical Design Inc.
Suite 120
200 Route 17 South
Mahwah
New Jersey 07430 USA
Tel: (201) 529 3323
Fax: (201) 529 2443
Please mention you heard about it from the Australian Distributor, Answers
>From Computers
--
>>Hugh Capper
>>email: "hughc' at \`extro.ucc.su.OZ.AU"
****************************************************************************
DESKTOP MODELER - User Info
----------------------------------------------------------------------------
Desktop Modeler Autocad
New product from Neil Ostlund, market by Autocad. Odd
combination, but the demos I saw Neil give at the fall
NY ACS were quite impressive. Very good performance
on a 486-based machine. Also available on SGI Indigo.
(PC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb &$at$& uunet.UU.NET
[It seems likely that this is the same as HYPERCHEM, but we are not able to
verify this!]
----------------------------------------------------------------------------
DESKTOP MODELER - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
KINEMAGE - User Info
----------------------------------------------------------------------------
Kinemage Protein Science Journal
Very simple, easy-to-use display program written
by Dave Richardson at UNC. Distributed free with
Protein Science Journal (brand new journal, very
good quality papers and science). Kinemage was
described in C&E News a few weeks ago - great program
for communicating medium-quality 3D images to the
masses. Not a model-builder, but good enough to
let non-specialist easily examine complex structures
and identify what's what, rotate them in real time,
measure distances, etc. There will probably be an
IBM PC version. I hope other journals will pick
this up; its a great idea. We're using it within
Chiron to distribute molecular models Spellmeyer and
I have built to other scientists for them to play with.
(MAC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb at.at uunet.UU.NET
----------------------------------------------------------------------------
KINEMAGE - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
LABVISION - User Info
----------------------------------------------------------------------------
Tripos also has a program called LabVision, for which I happen to have a
short blurb from this list: (See VENDOR INFO Section)
--
>>Steven W. Layten/Chemical Abstracts Service/ PO Box 3012, Columbus, OH 43210
>>INET: swl26 -8 at 8- cas.org BITNET: swl26 -8 at 8- cas UUCP:
osu-cis!chemabs!swl26
>># # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # #
----------------------------------------------------------------------------
LABVISION - Vendor Info
----------------------------------------------------------------------------
Tripos Associates has released LabVision. With LabVision you can quickly
compute spatial relationships, explore conformational possibilities, and
compute interactions between molecules such as proteins and ligands. Build,
visualize,analyze, and present molecular structures ranging from proteins,
nucleic acids and carbohydrates through inorganics and organics. LabVision
provides interfaceand file exchange with programs such as MOPAC,SYBYL, and the
Brookhaven ProteinData Bank. LabVision was specifically designed for use by
the bench scientist.It has pull-down menus and dialog boxes and is available on
a variety of workstations with PC/compatible and Macintosh extensions. Tripos
will be showing LabVision at the Atlanta ACS show.
--
>>Kathy Clark, Tripos Associates, 1699 S.Hanley Rd., St.Louis, MO 63144
***************************MACIMDAD***********************************
MacImdad Molecular Applications Group
(415)-857-0903
Commercialized version of Michael Levitt's software
for small and macromolecule building display. Very
impressive graphics, apparently quite powerful, but
non-intuitive interface. As hard to use as the big
workstation packages. Very expensive.
(MAC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb #*at*# uunet.UU.NET
****************************************************************************
MACMIMIC - User Info
----------------------------------------------------------------------------
MACMIMIC from ? written by Tommy Lilifors at Lund is supposed to be the cat's
meow. It runs on MACs and includes MM2 (?MMP2?) and maybe MM3. It's pretty
expensive I think.
--
>>"MARTIN' at \`cmda.abbott.com" "MARTIN%CMDA"
Others... The ACS has advertised at least one program in C&E
News, I think its called MACMIMIC. I haven't seen
it. I'm sure there are others out there, but I think
these are the major packages.
(MAC)
--
>>Jeff Blaney/Chiron/4560 Horton St./Emeryville, CA 94608
>>email: chiremv!andromeda!jeffb ( ( at ) ) uunet.UU.NET
----------------------------------------------------------------------------
MACMIMIC - Vendor Info
----------------------------------------------------------------------------
I am the author of MacMimic, a molecular modeling package that
runs on Macintosh II and Macintosh Quadra computers.
Some advantages of MacMimic:
o MacMimic is a complete Macintosh program;
It can handle multiple structures in multiple windows.
It prints on any color or laser-printer connected to the Macintosh.
You may Undo the last structural change. Etc.
o MacMimic has a powerful structure editor.
o MacMimic has built in chemical knowledge. Newly constructed models
are generally close (1-3 kcal/mol) to their local MM2 minima.
o MacMimic includes an authentic implementation of the molecular
mechanics program MM2(91). To the best of my knowledge there is
currently no other authentic implementations of MM2(91) for
personal computers.
o All computational options of MM2 such as dihedral drivers and
restricted motions have a user-friendly interface.
o MM2(91) has been expanded to handle 200 atoms and 80 PI-atoms.
o MM2(91) allows you to minimize a batch of structures.
o MacMimic is continuously being improved. We are currently working
on a Macintosh implementation of MM3 and an interface to MOPAC
(and maybe MOPAC itself).
MacMimic is used routinely by most of the Scandinavian pharmaceutical
industry. Furthermore, MacMimic is used by academic institutions and
industries in USA, Japan, Canada, and in several European countries.
I have sent some further information on MacMimic in a separate letter,
and I have asked Instar Software to send you a demo of MacMimic.
--
>>Anders Sundin e-mail: sundinKC()at()dna.lth.se
>>Organic Chemistry 2 Anders.Sundin -x- at -x- orgk2.lth.se
>>University of Lund ok2aps \\at// gemini.ldc.lu.se
>>P.O. Box 124 ok2aps - at - seldc52.bitnet
>>S-22100 Lund phone: +46 46 108214
>>Sweden fax: +46 46 108209
****************************************************************************
NANOVISION - User Info
----------------------------------------------------------------------------
The ACS sells Nanovision also for the MAC. It is a nice drawing program. One
can look at proteins as well as small molecules.
--
>>"MARTIN &$at$& cmda.abbott.com" "MARTIN%CMDA"
----------------------------------------------------------------------------
NANOVISION - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
NEMESIS - User Info
----------------------------------------------------------------------------
Oxford Molecular sells something called Nemesis I think. That I saw on the MAC
and it looked pretty nice for small molecules. Oxford Molecular, Oxford UK.
--
>>"MARTIN()at()cmda.abbott.com" "MARTIN%CMDA"
----------------------------------------------------------------------------
NEMESIS - Vendor Info
----------------------------------------------------------------------------
NONE
****************************************************************************
PCMCAD - User Info
----------------------------------------------------------------------------
PCMCAD is a polymer/biopolymer mechanics package from the same group that
markets GROMOS (a derivative of Amber).
--
>>"GERSON # - at - # DFWVM04.VNET.IBM.COM" "Dr. Dennis Gerson"
----------------------------------------------------------------------------
PCMCAD - Vendor Info
----------------------------------------------------------------------------
NONE
*************************************************************************
GENERAL INFORMATION - RECOMMENDED REVIEWS
-------------------------------------------------------------------------
regarding molecular modeling on a PC.....
There is a review article on this topic in Jour. CAMD, 2,(1988),81-90,
by Sadek & Munro. I am also aware of a large BASIC program in the book;
"Computational Chemistry; An Emphasis on Practical Solutions" by Milton Johnson,
Elsevier,1988. These are 2 places for you to look.
--
>>Gregory L. Durst
>>"DURST_GREGORY_L # - at - # LILLY.COM" "Greg Durst"
I recently saw a message from you that appeared on the OSC bulletin
board about PC based Molecular Modelling packages. I know of several but have
no real extensive experience with them. Some are: Chem3D (Mac based), MOBY (
PC) based, and PC-Model. However Phil Bayes just finished a sabatical year
at UNC-Chapel Hill specifically evaluating PC based Molecular Modelling
packages. His e-mail address is "pbays -8 at 8- bach.helios.nd.edu". (SEE BELOW
- FAV)
--
>>Raymond N. Dominey/Department of Chemistry/University of Richmond
>>dominey %! at !% urvax.urich.edu
I have a review of five programs for the Mac which appears in the
March (1992) issue of J. Chem. Ed. I have not yet received my copy,
but I understand that it is out. I have subsequently received
an updated version of Chem3D Plus. I would suggest that you
use that article as a starting point.....
--
>>"pbays <-at-> mozart.helios.nd.edu" "phil bays"
-------------------------------------------------------------------------
GENERAL INFORMATION - PKGS MENTIONED W/O COMMENT
-------------------------------------------------------------------------
A program you may wish to consider is the "Promodeler" package from
New England BioGraphics (1-802-633-4344). It is specifically designed for
macromolecules. Let me know if you have any technical questions about
specific capabilities.
--
>>Howard Holley
>>"HOLLEY (- at -) HUCHE1.HARVARD.EDU"
There are a number of packages available on PCs. I am more familiar with Mac
programs because I don't have an IBM clone.
1) Alchemy by Tripos
2) Nanovision by ACS software
3) Chem 3D ????
4) In addition, there are a number of shareware packages that I don't keep
track of. Macmolecule seems to ring a bell for one of them. I know that one
comes out of a group from Sweden.
--
>>Leonore Findsen/College of Pharmacy/University of Toledo
>>INTERNET: fax0357 (+ at +) uoft02.utoledo.edu
The best place to find a list of molecular modeling software that runs on PCs
would be the Appendices in Volumes 1 and 2 of Reviews in Computational
Chemistry. Don Boyd has written these appendices. (SEE BELOW - FAV) In
addition to the items that he has tabulated you should add Hyperchem, the new
release from Autodesk, Inc. They have run two page ads in Science and in C&EN
in the past few weeks and this week they are making their public announcement.
You can reach Autodesk at (800) 424-9737.
--
>>Roger DeKock/Department of Chemistry/Calvin College/Grand Rapids, MI 49546
>>DEKO -x- at -x- CALVIN.EDU
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
The following information comes from the appendix of the book "Reviews in
Computational Chemistry" written by K. B. Lipkowitz and D. B. Boyd.
This may not be a complete list. If you know of any other packages available,
please append them to this file.
-Dongchul Lim-
--
>>Steven W. Layten/Chemical Abstracts Service/ PO Box 3012, Columbus, OH 43210
>>INET: swl26;at;cas.org BITNET: swl26;at;cas UUCP:
osu-cis!chemabs!swl26
>># # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # #
--
Package: CAChe
Platform: Personal Computer
Address: Cache Group
Tektronics, Inc.
P.O.Box 500, Mail Stop 13-400
Beaverton, OR 97077
Phone: 503-627-3737
Description: Structure building, manipulation,MM2 energy minimization, stick,
ball-and-stick, or space-filling display, extended huckel
molecular orbital, electron density, and electrostatic maps,
3D viewing. Tektronics enhanced Mac-II.
Package: CAMSEQ/M
Platform: Personal Computer
Address: Weintraub Software Associates, Inc.
P.O.Box 42577
Cincinati, OH 45242
Description: Structure building, manipulation, rigid conformational searching
with interface to CAMSEQ/PC, stick, ball-and-stick, and
spacefilling display. PC.
Package: Chem3D+
Platform: Personal Computer
Address: Cambridge Scientific Computing Inc.
Dr. Stuart Rubenstein
875 Masschusetts Avenue, Suite 41
Cambridge, MA 02139
Phone: 617-491-6862
Description: Structure building, manipulation, simple force field and MM2
energy minimization, ball-and-stick and space-filling display.
Mac-II
Package: ChemCAD+
Platform: Personal Computer
Address: C_Graph Software, Inc.
P.O.Box 5641
Austin, TX 78763
Phone: 512-459-3562
Description: Structure building, manipulation, van der Waals and electrostatic
energy minimization by MM2 and MNDO, stick or ball-and-stick
display, report generation, interface to ChemFill.
PC. Also Macintosh Versions of MM2+ and MNDO+
Package: Desktop Molecular Modeller
Platform: Personal Computer
Address: Oxford Electronic Publishing
Oxford University press
Walton Street
Oxford OX2 6DP, U.K.
Phone: 44-865-56767, X4278
Description: Structure building, manipulation, energy minimization, stick,
ball-and-stick, or space-filling display.
PC.
Package: MM2, CNINDO/D, FORTICON8 (Extended Huckel), MNDO, HAM/3,
POLYATOM, MOPAC, DRAW, MOLVIEW, NAMOD
Platform: Personal Computer
Address: Quantun Chemistry Program Exchange (QCPE)
Department of Chemsitry
Indiana University
Bloomington, IN 47405
Phone: 812-855-4784
Description: Extensive catalog of programs for quantum mechanics, molecular
mechanics, and molecular graphics.
QCPE being academically affiliated provides software and
documentation at normal cost.
PC and Mac-II
Package: MOLIDEA
Platform: Personal Computer
Address: CompuDrug USA, Inc.
P.O.Box 202078
Austin, TX 78720
Phone: 800-877-0880
Description: Structure building, manipulation, van der Waals and electrostatic
energy minimization, CNDO/2 and other simple MO calculations,
interfaces to package for log P and statistics, stick, space-
filling, or dor surface display. QSAR and expert systems
programs.
PC.
Package: MicroChem
Platform: personal Computer
Address: ChemLab, Inc.
1780 Wilson Drive
Lake Forest, IL 60045
Phone: 312-996-4816
Description: Structure building, manipulation, energy minimization of organic,
inorganic and polymer units, stick, ball-and-stick, and space-
filling display, QSAR Craig plots.
Mac.
Package: NITRO
Platform: Personal Computer
Address: Tripos Associates
1699 Hanley Road
St. Louis, MO 63144
Phone: 800-323-2960
Description: Graphics processor for interfacing to SYBYL on a VAX, Mac-II, PC
versions. Alchemy does structure building, manipulation, SYBYL
energy minimization, stick or spave-filling display on a PC.
Alchemy-II interfaces to Chemical Abstracts Service registry
files.
Package: PCMODEL
Platform: Personal Computer
Address: Serena Software
Dr. Kevin E. Gilbert
P. O. Box 3076
Bloomington, IN 47402
Phone: 812-333-0823
Description: Structure building, manipulation, energy minimization by MMX (an
extension of MM2 and MMP1), stick and dot surface display, derived
from MODEL, handles inorganic as well as organic molecules, also
models transition states. Companion MOPAC 4.0 program.
Mac-II, IBM PC XT/AT, SGI, Apollo versions.
Similar Messages
06/08/1993: undergrad computational chem
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09/03/1998: Summary: looking for molecular modeling program on web or free-long!
10/01/1993: torsion of conjugated systems -- summary
02/16/1994: Request for Molecular Graphics Software-- Summary
07/01/1993: Summary on MM/MD
11/29/1993: Summary: HyperChem (SGI) replacements
05/03/1995: undergrad computational chem
05/03/1995: summary (II): teaching material for computational chemistry
04/05/1995: LogP
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