Subject: MacroModel

From: <[email-masked]>
Date: Fri, 21 Oct 94 17:13 GMT

Dear all,

Could someone please send me some information concerning MacroModel,
particularly the price to academics?

Lesley Adams
Centre for Molecular Design
University of Portsmouth
U.K.

---

From: "Peter Shenkin" <[email-masked]>
Date: Fri, 21 Oct 1994 14:34:29 -0400

On Oct 21,  5:13pm, <[email-masked]> wrote:
> Subject: CCL:MacroModel

> particularly the price to academics?

Hope the following is helpful;  please contact Joan Horgan directly for
pricing info.

	-P.

==========================================================================

		    INTRODUCTION TO MACROMODEL 4.5
			 September 21, 1994

        [[ You may obtain the latest version of this document remotely
            by means of "finger [email-masked]". ]]

Note:  MacroModel 5.0, due for release in early 1995, is in progress.
The SGI version will almost certainly require IRIX 5.x.  If this is
a problem, let us know.

We are now shipping Version 4.5 of MacroModel / BatchMin.  This version
is supported on SGI and on IBM RISC hardware;  BatchMin is supported
on several additional platforms.

This document contains the following sections:

	GETTING FURTHER INFORMATION:
	  Whom to contact for ordering information or for answers to
	  technical questions.

	NEW FEATURES IN VERSION 4.5:
	  Brief list of changes between version 4.0 and 4.5.  This 
	  section will be of greatest interest to users familiar with 
	  previous versions.

	PRODUCT DESCRIPTION (as of Version 4.0):
	  Brief description of the capabilities of the MacroModel,
	  BatchMin and XCluster programs.  (These three programs
	  are supplied as part of MacroModel)

	NEW FEATURES IN VERSION 4.0:
	  Differences between version 3.5 and 4.0.

GETTING FURTHER INFORMATION:

For ordering or pricing information for academic, government and 
non-profit sites, please contact:

	Ms. Joan Q. Horgan
	FAX: (212) 854-5429 or 678-9039
	Voice: (212) 854-8665
	Email: [email-masked]
	Address:  Box 663 Havemeyer Hall
	          Department of Chemistry
	          Columbia University
	          New York, NY  10027

Prospective industrial users should contact:

	Dr. Dan Chodosh / Distributed Chemical Graphics
	Voice:  (215) 885-3706
	FAX:  (215) 355-0954

Please address technical questions to:

	[email-masked] (note new host name!)
	FAX: (212) 678-9039
	Voice:  (212) 854-8402 (MacroModel)
	Voice:  (212) 854-5143 (BatchMin)

You may also address questions or share your experiences with the 
MacroModel user community by means of the MacroModel computer mailing list:

	[email-masked]  (Note: "02" is "zero two".)

Before doing so, you should subscribe to the list by sending mail that 
includes the line, "subscribe mmodinfo", to the address:

	[email-masked]

NEW FEATURES IN VERSION 4.5 (in addition to various bug-fixes):

        Front-end (MacroModel) features:
	        * MIPCAPI (MacroModel Inter-Process Communication
	          Application Interface) provides a library by means of
	          which programs written by users may utilize MacroModel
	          as a graphical front end
                * 1-D plots of energy vs. torsion angle
                * Ribbon diagrams for proteins
                * Visualization panels for associating specific
                  energetic interaction terms in the molecule with
                  specific lines in the force-field
                * Panel for more easily performing operations on sets
                * Panel for doing volume calculations on molecules
                * Panel for setting up BatchMin MC/SD calculations
	          (see below)
		* Button for setting up Monte-Carlo-Single-Minimum 
		  conformational searches
	        * Greater control and configurability of color scheme
	        * Movies from dynamics sampling now retain colors
	        * Ability to manually alter PDB chain, residue and
		  atom names

        Back-end (BatchMin) features:
		* Free-energy perturbation;  works with mixed-mode
		  Monte-Carlo / Stochastic Dynamics, as well as with
		  SD or MD.  Implemented for network-distributed
		  execution, if desired.
                * Facilities for re-initializing conformational
                  searches from the output of previous, incomplete 
		  searches, and for obtaining interim summaries of 
		  the progress of a search, so far.
                * "ASET" command for defining sets of atoms, and 
		  printing energetic contributions within and between 
		  the sets.
                * User-definable atom types, read in at run-time.  We
                  supply new types and force-field components for alkali
                  metal cations, but users can also add their own types,
                  and supply parameters for these types in the force-
		  field.
		* Additional capabilities for handling geometry-dependent
		  force-field parameters. This will be useful mostly for
		  transition-state modeling.  MM2* additions: Force-field
		  parameters for transition-state models of activated
		  Diels-Alder reactions, nitrileoxide additions (K. Houk);
		  sulfonamide parameters (G. Poli);  more parameters for 
		  boron-containing transition states (A. Bernardi).  AMBER*
		  and OPLSA* addition: pyranose parameter revision for
		  acetal anomeric equilibrium (Q. McDonald);  new
		  parameters based on unpublished work by P. Kollman (UCSF)
		  for gem diethers such as dimethoxymethane.

PRODUCT INFORMATION:

	MacroModel is the generic name for a set of molecular modeling
	tools; it actually consists of several separate programs.  

	MacroModel itself is a visualization tool for building, examining
	and manipulating organic and biological molecules.  It can read
	and write molecular files in its own format, as well as in the 
	format specified by the the Protein Data Bank at Brookhaven 
	National Laboratories.  A number of other programs are capable
	of writing MacroModel format files;  these include Gaussian-92
	and Chem-3D.

	BatchMin is a separate program which carries out molecular
	mechanics.  Most users are never aware of the separate existence
	of BatchMin, since most BatchMin jobs are set up, and the
	results monitored, by means of its interface with MacroModel.
	Thus, most users think of MacroModel and BatchMin as one;  we
	will refer to them together as "MacroModel" in the rest of this
	description.

	One of MacroModel's strengths is the fact that it provides
	the user with a choice of implementations of the AMBER, MM2,
	MM3, and OPLS force-fields.  The force-field which has
	been best parameterized for the system in question can be
	used (MM3 for gas-phase study of hydrocarbons, AMBER for 
	peptides and nucleic acids, OPLS for solvated organic
	molecules).  The force-field of choice is read in at run-
	time;  its file format is such that the user can alter general
	parameters at will, or add parameters for molecular substructures 
	which have either no parameters or only poorly defined parameters.  
	For example, charge distributions derived by the user
	from ab-initio quantum studies on a system of interest can be 
	used in MacroModel to perform molecular-mechanics studies of 
	the same system, instead of using the force-field's default
	parameters.

	A list of molecular mechanics procedures supported by MacroModel
	follows.  For each method, the user may select from among the
	choices given in parentheses. In most cases the program
	selects a reasonable default if an explicit choice is not made.

		Conformational search (systematic; Monte-Carlo)
		Energy minimization (steepest descent; variable metric;
		 conjugate gradient; truncated Newton; full-matrix
		 Newton-Raphson)  In multiple structure minimization 
		 mode, the program eliminates duplicate output structures
		 from the results of minimizing a sequence of input
		 structures.
		Monte Carlo sampling
		Molecular dynamics (constant energy; constant temperature;
		 bath-coupled stochastic dynamics) SHAKE is available.
		Mixed-mode Monte Carlo / Stochastic Dynamics.  This is
		 a procedure developed here which speeds up the sampling
		 of conformational space during a dynamics run generating
		 a canonical ensemble.
		Solvation.  We provide a continuum model of solvation
		 known as the Generalized Born / Surface Area (GB/SA)
		 model.  This provides good approximations to relative
		 solvated energies at a computational cost much lower
		 than that of explicit solvent models.  We provide
		 parameterization for water and for chloroform.
		Free-energy perturbation, in the context of implicit
		 solvent and mixed-mode SD/MC.

	XCluster performs cluster analysis on molecular conformations.  
	For example, the structures resulting from a conformational 
	search may be examined to determine whether they fall into 
	distinct classes.  Though a separate process, this program is 
	equipped to communicate with a running MacroModel process.  For 
	example, a subset of atoms to be compared for conformational 
	similarity may be "picked" from the MacroModel interface and 
	automatically passed to XCluster.

	In all of these, as well as new procedures being developed,
	we are committed to full disclosure of methods and parameters
	by means of prompt publication.

	MacroModel runs on Silicon Graphics or IBM/RS 6000 hardware 
	equipped with GL graphics.  Minimum suggested hardware 
	requirements are:

		SGI: 32 Mb main memory, 1.2 Gb disk drive.  
		IBM: 64 Mb main memory, 1.2 Gb disk drive.

	If you plan to study large molecules, such as proteins, we
	recommend that you configure your system with 100 Mb of
	swap space.

        -----------------------------------------------------------------------
        For MacroModel to run on an SGI machine you need to have (in
	addition to the standard libraries) the following software 
	products loaded:

		C++ run-time environment (to use the 
			Force Field Parameter Viewer)

        -----------------------------------------------------------------------
	For IBM machines we support the following graphics adapters: 
	24 bit Sabine with zbuffer or 24 bit gt4x with zbuffer.
	We do not guarantee that other boards will work properly.	

        For MacroModel to run on an IBM RS/6000 you need to have the 
	following software products loaded:

		X/Motif run-time environment
		FORTRAN run-time environment
		GL run-time environment
		C++ run-time environment (to use the 
			Force Field Parameter Viewer)

	These products may be purchased from IBM.

NEW FEATURES IN VERSION 4.0:

MacroModel Version 4.0 includes the following new features:

	Front-end (MacroModel) features:
		* Improved Help facility
		* Ramachandran plots
		* Ability to analyze ensembles of structures based on
		  miscellaneous collective features (e.g., centroid of
		  a group of atoms)
		* "Filter panels" providing the ability to select structures
		  meeting user-defined selection criteria from a file of
		  multiple conformations.
		* Support for hardware stereo on SGI
		* Improved conversion to and from PDB format files

	Back-end (BatchMin) features:
		* Support for monitoring H-bonds during dynamics
		* Mixed mode Molecular Dynamics / Monte Carlo
		* Network-distributed parallel processing for 
		  conformational search and multiple minimization
		* Built-in tools for static memory analysis
		* Improved tools for source-code maintenance (relevant
		  only to industrial source-code customers)
		
	XCluster:
		* An entirely new program, XCluster, which performs
		  cluster analysis on ensembles of molecular conformations

-- 
*********** World music:  What bluegrass is to a Bulgarian. **********
*Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,*
* New York, NY  10027;     [email-masked];     (212) 854-5143  *
************ Alphabetical order makes strange bedfellows. ************