From:	ZSYAMP01%EBCESCA1.BITNET-0at0-phem3.acs.ohio-state.edu
Date:	Thu, 01 Jul 1993 09:47:41 +0100 (CET)
Subject:	Summary on MM/MD

    Dear netters,
                 Here is the summary about MM/MD packages i promised 4
months ago (I'm sorry for the delay). It has been 'upgraded' with the
opinions of my own users. Although I tried to abstract, it is going to
be very large, so here are the main points:

    - All what I'm going to say is for supercomputers
    - I have not considered quantum mechanics programs (i.e. GAUSSIAN)
    - Every computational program (running in a supercomputer)
      needs a good visualization interface (running in a WS)
    - It is necessary to to consider three main groups of programs:
     'small molecules', 'general purpose', and 'large molecules' ones.
    - Commercial programs: recommended for simulations; expensive;
      code not available; good support
    - Academic programs: recommended for basic research; cheap; code
      available; support not guaranteed

    And here comes the summary.
                                               Alicia Martinez
                                            Supercomputation Center
                                                of Catalonia

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: Daniel Ripoll 

There are three major companies in US with molecular modeling packages in the
market:

Biosym (Insight-Discover), Molecular Simulations (QUANTA), Tripos Inc.(Sybyl).
These three packages provide many basic features that are very similar.
All af them will allow you to carry out molecular mechanics and dynamics
simulations. They differ mainly in the force field they used for the energy
calculations.

Each of these programs have their own strength that make them suitable for
particular type of applications. Among the ones I know, Sybyl (Tripos Inc)
is very good on studies of small molecules.

The BIOPOLYMER module has many interesting features useful for protein studies.

QUANTA (with Charmm) is very good for studies of protein dynamics.
These vendors also provide tools like XPLOR that are extensively used in
Macromolecular structure determinations using X-ray crystallography and
Nuclear Magnetic Resonance (NMR).

Discover (Biosym), as I understand, is a very well developed force field and the
molecular dynamics program is very robust and fast.

For studies on small molecules, there is another important program you should
consider named MACROMODEL. This program is being developed by Prof. Clark Still
from Columbia University). It uses the MM3 force field. The code is being sold
at very low price for academic users by Columbia University.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: CVINALS #*at*# BNANDP51

(...)I'm most satisfied with Discover (Biosym). It's a complet program
(along with Insight) adapted to the beginner (user-friendly)
as well as to the expertise.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:         Willem Vermin 

(...) I think that QUANTA/CHARMM is a
good choice. As you probably know: QUANTA runs on a workstation, CHARMM
can run on a cray or ibm mainframe.
(...)
And , of course, you have to lsiten to the users of your system. If they
really want DISCOVER, I think there is only one thing to do: buy it!

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:         UGLIENGO \\at// CH.UNITO.IT

(...) I strongly recommend GROMOS CHARM and AMBER just to cover the
field of biological molecules.
We have the BIOSYM package here in Torino running on a SGI35;
we joined the Catalysis and Sorption project two years ago so that we
got a large discount. Even so, the package cost a lot of money for our
standard. It is very well documented and frequently updated.
(...)
My point of view is that make no sense to buy DISCOVER alone without
the graphic package. It is certainly possible to have it running
on a CRAY and get the result on a remote INDIGO running INSIGHT.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:         "Gabor I. Csonka" 

The reply to your question: there is a new software called Hypercem
which seems to be very good package. Another thing I can suggest is
Macromodel. The Sybill force field of Tripos is also worth mentioning.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:         Caterina Ghio 

1) INSIGHT and DISCOVER are expensive, but they are very friendly to use. In
   a routine work they are helpful.
2) SYBYL (Tripos Associates), another visualization software, is slightly
   cheaper, if it is still so. In any case you can ask for a short period
   trial for both SYBYL and INSIGHT/DISCOVER. Usually for 2 months.
3) Harel Weinstein (Mount Sinai Hospital, CUNY) prefers using CHARMM and
   QUANTA for small systems, and AMBER/SYBYL for larger ones.
4) MidasPlus is a cheap package of the Computer Graphics Lab of the University
   of California, San Francisco. It costs about $300. The upgrade is $50. It is
   a very good program for visualization and can be used with any simulation
   software, even though AMBER is suggested. It has no pop-up menus, but the
   commands can be sharply abbreviated. e-mail NORMA at cgl.ucsf.edu
5) Be sure to buy a workstation allowing you to see stereo pictures. When deal-
   ing with large systems it is impossible to do without. Both MidasPlus and
   Insight or SYBYL have the stereo option. We have an SGI 4D-GTXB with stereo.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: Max 

Sybyl has many good functions and is the best for small molecules
(it isn't so good for proteins or nucleic acids).
(...)
Insight/Discover is better than Sybyl for large molecules and           n
'solvent box' simulations; the same applies to Quanta/Charmm.
(...)
A package which seems also good for visualizations id AVS, distributed
by Molecular Simulations.                                                  SI),

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: ross()at()cgl.ucsf.edu (Bill Ross )

The main differences I know between Amber and commercial packages are:

Amber:

 - comes as source code, so you can do your own development.
 - is probably much cheaper (see prices below).
 - does not have a released graphics interface yet (one is on the way).
   Meanwhile, a graphics program that reads and writes Protein Data
   Bank format files is needed (I believe free ones for SGI are obtainable).
 - is strong in normal mode and molecular mechanics-based methods but
   has no quantum, docking, qsar, or other different methods incorporated.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: (Dr.) Dave Winkler 

I'm a 'small molecule' molecular modeller
(i.e. drugs and crop protection chemicals).  I find the Sybyl software from
Tripos Associates, St. Louis very good.  (..)
It is a very comprehensive suite
of programs which do all of the required functions, and, very importantly, the
software is very easy to use.  They hve one unique advantage over other similar
packages such as Biosym and MSI in that they have ComFA analysis (comparitive
molecular field analysis (patented)).  They also have a very useful molecular
spreadsheet which integrates all of the modelling, database and biological data
into a very useful form dor analysis (it is easy to 'drown in data' otherwise).
Their Unity molecular database package is the only alternative to the widely
used but ancient MACCS database.

If cost is a factor, then Chemical Design's CHEM-X molecular modelling package
is also very good.  They also seem to be a little ahead of the other companies
in bringing new, innovative design methods into the market place.  You can
email them too (Chemdesign : at : applelink.apple.com).

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: Sophie Creuzet C3NI IBM/CNUSC 

CHARMm   (which was developped by Karplus group)   was initially done for
proteins and is presently the best you can find for simulations concerning
proteins. You'll  find  hundreds of publications using CHARMm and this is
not only a   proof that it is scientifically valid but a mine of previous
calculations very helpfull for people begining in this field.

AMBER (developped by Kollman's group) is the next in my list since its
story is very similar to CHARMm's one. But it has originally been
developed for nucleic acids, and it's probably the best for that.
In fact, both Karplus and Kollman decided to develop parameters for
proteins and nucleic acids so today people are using them almost
indifferently.

However AMBER is almost free and CHARMm rather expensive, I think CHARMm
is more popular. I think it's a question of functionalities as well.
Moreover, you have a good interface for CHARMm (QUANTA) which doesn't
exist for AMBER. Since a graphical interface is very important when you
deal with macromolecules this is also a reason why CHARMm is prefered.

DISCOVER (developed and sold by BIOSYM) seems to become more and more
popular. I can't say anything concerning it's reliability since the
number of paper using it is really weak compared to CHARMm or AMBER.
The interface (INSIGHT which is among the best) seems to be one of its
trump cards.

Finally, MSI as well as BIOSYM have very good package for RMN for
example, which is also a hudge consumer of computing power.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:     "T. Mark Reboul" 

Inexpensive but useful alternatives you might consider are:

MacroModel -- mmod' at \`cuchmc.chem.columbia.edu -- for modeling

Grasp -- nicholls -x- at -x- cuhhca.hhmi.columbia.edu -- for visualization

These are non-commercial but well-maintained products which are fairly
inexpensive, maybe ~$500 each.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: dobbskd[ AT ]esvax.dnet.dupont.com

(...) The best approach is to have a good
understanding of the problems that you want to solve over the
next few years and then talk to other computational people about
the best way to tackle these problems with existing software. It
would not be a good idea to try to buy the "best" software (all
simulation software falls in this category depending on who you
talk to), install it, and then expect your users to do "wonders"
with the software (this scenario is greatly pushed by your more
visible software vendors).

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: nauss;at;wrair-emh1.army.mil

I have extensive experience with QUANTA and CHARMM.  Generally, CHARMM is an
adequate program to use.  It is very flexible once one knows the commands.
(...) I would recommend CHARMM as a stand alone program.

QUANTA, however, has problems: (...)
the dialog boxes (...) changing the display (...) MSI's hotline
(...) Their documentation (...)
After having used QUANTA for three years now, I am not pleased with it.

I have used an old version of SYBYL from Tripos.  I was not pleased with it
either as the organization of menus was not intuitive.
(...)
What I have seen of INSIGHT and DISCOVER I like.  The menus have a good feel to
them, selections are generally where I expect them to be. Also, INSIGHT seems
to be better integrated with the operating system.
(...) As far as how powerful DISCOVER is, I am not certain.
However, Biosym seems to document
their product much better than MSI.  Also, Biosym has published their tests of
the DISCOVER force field in the open literature.  MSI has not although the
original CHARMM from Harvard is well documented.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:    SOARES <-at-> XRAY.BMC.UU.SE

If simulation techniques are an auxiliary tool for your work, I
would suggest a commercial package, like Discover,
Hyperchem, Prosimulate, etc. If however, people are going to
do more fundamental research on the field of Molecular
dynamics, an open code would be more adequate.
(...) In this latter group I would recommend
GROMOS or AMBER. We are using GROMOS here in my group and for
visualization of trajectories we use the program mdFRODO,
which accepts GROMOS outputs. The mdFRODO program is
distributed by Dr. Olle Nilsson, and with it is also
distributed the NICE package which performs numerical
analysis of MD results.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From:    F0418950;at;JAGUAR.CSC.WSU.EDU

Having used INSIGHTII/DISCOVER for about 3 years now I conditionally recommend
it as a good molecular mechanics/dynamics package.
(...)
I would suggest looking in depth at the capibilites that it has and see if
they fit your needs, AS THEY EXIST IN THE PROGRAM ALREADY.  If your center plans
to go beyond the choices the program gives and develop your own algorithms or
install new ones, Insight/Discover is not a good choice (in my opinion).
It is too much of a packaged program and adding things to it is very hard.
CHARMM on the other hand, is harder to use but extremely adaptable.
(...)
For research and development, look at CHARMM.  For routine use, look at
Insight/Discover.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: MARTIN%CMDA 

I strongly suggest that you get a copy of SYBYL for your SG's.  We have
just moved from in-house molecular graphics to SYBYL & find that the
Windows-based environment & the Sybyl Programming Language make it very
easy to interface applications & keep everything straight.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: 

We are using AMBER and I think it needs a
user-friendly environment to manipulate the results:
    MIDAS (UCSF)
    QCPE 623 "MD Display".
    QCPE 627 "X11-based AMBER MD viewing/analysis program".
(...)
Maybe Quanta/Charmm would be good to invest in because AMBER
works basically with proteins, whilst CHARMM is also good for
small molecules (of course it's much more expensive).
(...)

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From: JSCHELDE %! at !% STEEVAST.RUG.AC.BE

I'm planning to buy Charmm because of its flexibility
but I will first try it out.


Similar Messages
06/08/1993:  undergrad computational chem
04/13/1992:  PC-BASED MOLECULAR MODELING PACKAGES
06/28/1995:  Re:POSTED RESPONSES: Quantitative assessment of novel ligands
02/16/1994:  Request for Molecular Graphics Software-- Summary
10/01/1993:  torsion of conjugated systems -- summary
05/03/1995:  summary (II): teaching material for computational chemistry
04/08/1994:  normal coordinate calculation 

09/03/1998:  Summary: looking for molecular modeling program on web or free-long!
12/20/1994:  Re: CCL:Dendrimer modelling
02/21/1996:  Summary: CRYSTAL & all


Raw Message Text