> From chemistry-request@www.ccl.net Thu May  1 02:21 EDT 1997
From: "Peter Shenkin" 
Message-Id: <9704301742.ZM4595@still3.chem.columbia.edu>
Date: Wed, 30 Apr 1997 17:42:50 -0400
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
To: CHEMISTRY@www.ccl.net, mmodlist@chem.iupui.edu
Subject: CCL:Announcing MacroModel 6.0
Sender: Computational Chemistry List 
Errors-To: ccl@www.ccl.net



MacroModel 6.0 has been released.  Information is available at:

	http://www.columbia.edu/cu/chemistry/mmod/mmod.html

MacroModel is a general-purpose molecular modeling package developed
at Columbia University.  We support several force fields and a variety
of molecular-mechanics procedures.

Here are a few features that are new in Version 6.0:

	Manuals supplied in HTML as well as PostScript and hard-copy form.
	 HTML manuals can also be browsed at our WWW site.

	Support for some additional hardware options (newer 3D-graphics
	 boards under AIX, better R10000 optimization for SGI).

	MacroModel (GUI): Visualization of normal modes.  Interfaces
	 to several new computational procedures.  Enhancements to the
	 atom-set language.

	BatchMin (computational engine): Low-mode conformational search 
	 method of Istvan Kolossvary.  Fully frozen atoms.  Faster GB/SA
	 solvation calculations.  Generate normal-mode movies for
	 visualization.

	Xcluster (conformational cluster analysis): Average structures.
	 Write out Average, Representative or Superimposed conformations
	 for a single cluster (or all clusters) at any hierarchical 
	 clustering level.  Some new interactive features in the 
	 visualization tools.

Academic users may order using the on-line order form.

Enjoy!
-P.

	

-- 
************* "The past ain't what it used to be" (M. Reboul) *************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  shenkin@columbia.edu;  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

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

		    INTRODUCTION TO MACROMODEL 5.5
			     May 1996

        [[ You may obtain the latest version of this document remotely
            by means of "finger mmod@still3.chem.columbia.edu". ]]


Please browse our home page using your favorite www browser:

     http://www.columbia.edu/cu/chemistry/mmod/mmod.html

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 5.5:
	  Detailed list of new features that are in version 5.5.

	PRODUCT DESCRIPTION (as of Version 5.5):
	  Brief description of the capabilities of the MacroModel,
	  BatchMin and XCluster programs.  (These three programs
	  are supplied as part of MacroModel)

	HARDWARE REQUIREMENTS
        NEW FEATURES AS OF VERSION 5.0:

--------------------------------------------------------------------------

GETTING FURTHER INFORMATION:

For ordering or pricing information for single-user academic licenses
please contact:

	Ms. Joan Q. Horgan
	FAX:   (212) 854-5429 or 854-4213
	Voice: (212) 854-8665
	Email: jqh@still3.chem.columbia.edu
	Address:  Box 663 Havemeyer Hall
	          Department of Chemistry
	          Columbia University
	          New York, NY  10027

Ordering or pricing information for commercial, non-profit, 
government or academic departmental licenses should be gotten by contacting:

	Dr. Carol Parish
	Voice:  (718) 981-7875
	FAX:    (718) 981-3559
	Email:  carol@still3.chem.columbia.edu

Please address technical questions to:

	E-mail: mmod@still3.chem.columbia.edu (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:

	mmodlist@chem.iupui.edu

Before you do this, you should subscribe to the list by sending a
request to the list administrator, Dan Robertson of Purdue University,
at the address:

	mmod-request@chem.iupui.edu

Dan administers the list manually, so please state your request
("Please add me to the list", or "Please delete me from the list", or
whatever) in plain English.

--------------------------------------------------------------------------
			NEW FEATURES IN VERSION 5.5

General:
   * Ability to automatically start-up the BatchMin Server when rebooting an
     SGI machine.

MacroModel:
   * ASL Panel. The Atom Specification Language Panel provides an easy to
     use mechanism for defining sets of atoms via a simple textual command
     line specification language. This panel can be used while in any mode
     (unlike the SETS mode which is limited to being in ANALYZ/SETS). Users
     may use the panel to specify sets based upon various atom, residue, and
     molecule criteria. The ASL will be of particular interest to users of
     MacroModel who work primarily with bio-polymers as the ASL provides
     tools to specify sets of atoms based on familiar concepts such as chain
     name and residue type. The panel can be used from within any submode of
     MacroModel once it is displayed.
   * Automatic selection of X Windows resources when starting up MacroModel.
     The macromodel script is now "smart" and selects the appropriate
     resources depending on the resolution of your display.
   * Interface to Amber 94 provided.
   * Interface to MMFF (Merck-Molecular Force-Field) provided.

BatchMin: 
   * All force-fields now use, by default, a dielectric constant of unity
     when computing coulombic interactions. Previously, the default for
     AMBER*, MM2* and MM3* was to use a distance-dependent dielectric. The
     new default is more appropriate for comparison with gas-phase quantum
     chemical calculations or experimental data, and solution-phase
     computations are better done using the GB/SA model (though MM2 and MM3
     are not well-suited for this treatment).
   * Amber 94 All Atom Parameters
   * MMFF (Merck-Molecular Force-Field)

--------------------------------------------------------------------------

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.  We also supply converters for Sybyl Mol2 format.

	Some facilities of the visualization front-end are:

		- Molecular builder (organic, peptide, nucleic-acid and
		  carbohydrate modes)
		- 3-D rotation and translation facilities with either
		  the X or the GL interface;  in GL (on IBM RISC or
		  SGI), space-filling representations (ball & stick,
		  CPK, polytube, ribbons for proteins).  Hardware stereo
		  is supported on SGI.  
		- Setup and monitoring of energetic (BatchMin) processes.
		  MacroModel can initiate, monitor, disconnect from and 
		  reconnect to multiple processes on networked hosts.
		- Help facility explains energetic procedures as well
		  as visualization commands.
		- 1D and 2D (Ramachandran) plots of energy vs. torsion angle.
		- Display of selected distances, bond angles, torsions,
		  hydrogen bonds in GL mode.
		- Interactive rotation of torsions or of individual molecules
		  in GL mode.
		- Least-squares superposition of pairs or sets of
		  conformers.
		- Definition of atom sets for use by other commands
		  (display/undisplay, color, ribbons, etc.) and for
		  use in setting up energetic procedures (e.g., list
		  of atoms to fix in place during dynamics).
		- Calculation and display of surfaces and volumes.
		- NMR coupling-constant calculations.
		- Structure-file filtering:  selects structures meeting
		  predefined criteria from a multiple-conformation 
		  structure file. "Virtual atoms" at centroid of
		  select4ed atoms can be used in defining criteria.
		- Configurable color scheme.
		- MIPCAPI code library, supplied to all customers,
		  allows MacroModel to be used as a front-end for
		  programs written by users.
		- MMIO code library, supplied to all customers, allows
		  user applications to read and write MacroModel
		  structure files easily and portably.
		
	Molecular mechanics calculations are carried out by a separate
	program called BatchMin.  These calculations are usually set up 
	and monitored by the MacroModel front end, but BatchMin input
	can also be prepared by hand, and BatchMin can be run as a
	stand-alone process.  

	Some of BatchMin's capabilities are:

		-Choice of AMBER*, MM2*, MM3*, OPLSA* force-fields 
		 These are our emulations of native AMBER, MM2, MM3
		 and OPLSA.  Parameters are read in at run time from
		 files that the user may alter in order to add new
		 or revised parameters.  Parameters may be limited
		 to substructures specified by a SMILES-like notation.
		 Geometry-dependent parameters are supported, as are
		 user-definable atom types. 

		 As of 5.5 we also support the AMBER94, and MMFF force-fields.

		-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.  Molecular symmetry is taken into account.
		-Conformational search (systematic; Monte-Carlo)
		 A new search can be initiated with the results of
		 an earlier one, and an interim summary of a running
		 search can be triggered at any time.
		-Metropolis Monte Carlo simulations
		-Importance sampling speeds up Monte Carlo procedures.
		-Molecular dynamics (constant energy; constant temperature;
		 bath-coupled stochastic dynamics). SHAKE is available.
		 Distances, torsions, hydrogen bonds, etc. can be monitored
		 during dynamics.
		-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.
		-Network-distributed processing on a network of
		 possibly heterogeneous workstations.  Procedures
		 supported:  free-energy perturbation, conformational
		 search, multiple minimization.

	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 using
	the MIPCAPI, described above.  For example, a subset of atoms 
	to be compared for conformational similarity may be "picked" from 
	the MacroModel interface and automatically passed to XCluster.

	XCluster's capabilities include:

		-Operates in torsional space or in Cartesian space.
		 If Cartesian, pairwise rigid-body optimal superposition 
		 of structures may be selected or deselected.
		-A subset of the atoms (e.g., only ring atoms) can be
		 used as the basis for clustering.
		-Takes molecular symmetry into account.
		-Can also operate on a user-supplied distance matrix.
		-Operates from X interface or as a batch job.  The interface
		 can be used to examine the results of a batch job.
		-Interactive visual display of color-coded pairwise distance 
		 matrix.  A mouse-click on a pixel displays the 
		 characteristics of the structure pair associated with that 
		 pixel.
		-Implements the single-link hierarchical clustering method.
		 "Mosaic" display (similar to dendritogram) displays entire
		 clustering hierarchy and also allows mouse interaction.
		-Plots of clustering statistics vs. clustering level allow
		 selection of best clustering in the hierarchy, and a
		 determination of whether or not the data are indeed well
		 clustered or not.
		-Structure files, optimally superposed to exhibit the
		 clustering, may be written out for visualization in
		 MacroModel.  Alternatively, a single representative
		 structure from each cluster may be written out.

--------------------------------------------------------------------------
HARDWARE REQUIREMENTS

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

		SGI: 32 Mb main memory, 1.2 Gb disk drive, IRIX 5.2
		IBM: 64 Mb main memory, 1.2 Gb disk drive, AIX 3.2.5

	If you plan to study large molecules, such as proteins, we
	recommend that you configure your system with 100 Mb of
	swap space.  On SGI, we also recommend a large amount of 
	"virtual swap space."  The actual distribution file set
        will require 70MB of disk space.

	In addition to the above platforms, BatchMin, only, runs
	on Convex, HP, Cray, Fujitsu, and IBM SP2.

        -----------------------------------------------------------------------

	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 as
        we have not test other boards.  Please note that AIX 4.1
	has dropped support for the Sabine board.  To use this board
	you must be at AIX 3.2.5.

        For MacroModel 5.5 to run on an IBM RS/6000 you need to have the 
	following software products loaded:

		X/Motif run-time environment
		GL run-time environment

	These products may be purchased from IBM.

--------------------------------------------------------------------------

			NEW FEATURES AS OF VERSION 5.0

General:

	Compressed ASCII file format affords up to 2.5-fold disk-space
	savings for multiconformer files (more if SUBS/FXAT is used).  
	All MacroModel programs are capable of reading this new format.
	-  Converters are supplied for conversion to/from compressed format.
	-  An "MMIO library" is supplied which can be linked to 
	   user code.  Programmers can link to this library to read
	   / write MacroModel data files (compressed or uncompressed
	   format) into / from their own code.  This library
	   should be used by all application developers to read/write
	   MacroModel structure files.

	Converters are supplied for mmod <--> SYBYL_mol2 format.

	An additional document, "MacroModel Technical Notes", is
	supplied.  This contains descriptions of force-field 
	parameters recently derived, descriptions of MacroModel 
	libraries (such as the MMIO library and the MIPCAPI library), 
	and usage notes for advanced simulation methods.

	Mmod/bmin communication (including rbmin and dbmin) has been
	converted from the low-level socket to the higher-level RPC 
	protocol.  This completely replaces the socket-based method.
	One consequence of this change is that network-distributed
	BatchMin jobs no longer require a special startup script;
	they may now be started like any other job.


MacroModel:

Many of the following new features are more fully described in the 
MacroModel User's Manual.  Also, all changes to the front-end are 
described in $MMOD_ROOT/mmod.doc.  

	Pixelmap PostScript plotting in GL mode. WYSIWYG -- 
	What You See Is What You Get -- plotting of everything 
	exactly as it is in the 3D window (CPK. Ball+Stick, 
	ribbons, etc. get included). Includes the Control Window 
	unless it is explicitly TURNED OFF.

	Graphics now uses mixed-model programming.  This speeds up 
	the graphics substantially and minimizes cpu utilization.

	New remote BatchMin programs. These are RPC-based. The new
	programs are rbm, and bminrd which replace rbmin and bmind,
	respectively. The mmdbmin library has the same name but has
	been rewritten. Also, the new RPC-based client/server code
	is NOT compatible with the old socket-based client/server
	code. Run only the new RPC-based code. See the MacroModel
	Users Manual for installation details.

	PhotoMode. Accessed by hitting F1 in GL mode. Expands 3D
	window and removes border. Toggle back out by hitting F1
	again.

	Wire frame PostScript plotting now sorts bonds by z
	midpoint giving correct bond overlap. Also, user can choose
	to plot by bond order or by depth cue. These determine the
	drawn line's width based on order of the bond or the
	distance from the user, respectively.

	Plotting of RGB files on SGI machines in GL mode has been
	added. Accessed via PLOT in ANALYZ. This is also WYSYWIG
	plotting.

	Ribbon plotting can now be done on just a working set
	(instead of all the atoms in the connection table).

	Interfaces are provided to the new BatchMin VDWB and
	LIGB commands.

	In 3D mode the buttons for Torsional rotation, and
	molecular transformations have been moved into the Control
	Window.

	SYSTEM button replaces TTY button. Users can put their own
	programs in the pop-up list via the system.dat file. The
	defaults include an xterm (TTY) and xcluster.

	FIFO restrictions no longer apply. Users can run as many
	MacroModels in the same directory as they wish.

	Set Colors panel in addition to current RGB sliders now
	allows for choosing colors by name.

	Movie now allows user to color atoms by atom type or
	force-field gradient.

        HBond button in ANALYZ mode, which hightlights hydrogen-
	bonds, now uses more sensible defaults for distance and
	donor and acceptor angles.  The defaults can be configured
	using the HPref button.

	FilMol, SelMol buttons put into SUBSED. These are similar
	to the FilRs, SelRs buttons as they allow the user to fill
	out a molecule or select a molecule for inclusion into the
	current shell or the substructure.  This is useful to 
        add an entire inhibitor molecule to the list of atoms to
        be fully considered in energetic calculations.

	Half-width flat bottom constraint option added to CNSTR
	(constraint) mode for constraining atoms to a region around
        an "anchor point".

	Help button placed in the top portion of the Main Button
	Panel. Button-specific help can still be gotten by clicking 
        with the right mouse button over any Main Panel button.

	Additional ribbon method:  shaded curve plotting creates 
        smoother ribbons with fewer guide points.


BatchMin: 

New commands and changes to existing commands are described more
fully in the BatchMin Reference Manual.

	Importance sampling ("jumping between wells") speeds up
	Monte Carlo procedures both in MC (MCLO) and mixed mode 
	(MCSD) simulations. The importance sampling method is
	especially useful for ring systems. See the Primer,
	the technical manual and the IMPS, IMPO and ITOR 
	commands in the BatchMin manual.

	Velocity verlet dynamics: speeds up and permits higher
	acceptance ratios for MCSD (mixed mode) calculations; 
	used for all dynamics.

	ASNT command: turns off interactions between atom sets.

	New commands are added to facilitate the modeling of inorganic
	complexes.  The VDWB command replaces bend interactions about
	a metal atom with 1-3 nonbonded interactions;  this allows modeling
	of the coordination sphere using the "points on a sphere" model,
	which is philosophically grounded in VSEPR.  The LIGB command
	allows specification of bonds to be broken during conformational
	search.  This allows a "configurational search" to be performed
	about the metal.  For energetic modeling using conventional
	force-field interactions (explicit bend parameters about the metal),
	force-field substructures may now specify an angular dependence
	of parameters;  for example, if an L-M-L bond is initally
	close to 120 degrees, it may be given at minimum at 120 degrees,
	to model a pair of equatorial ligands in a trigonal bipyramidal
	complex.

	Full AMBER-style torsional offsets have been implemented.
	This allows specification of separate offsets for each Vn
	term, and allows arbitrary values for the offsets (i.e.,
	one is not limited to 0 or 180 degrees).  See Appendix 3
	of the BatchMin manual for details.  This increased 
	flexibility will allow better fitting of torsional energies
	obtained from quantum mechanical calculations.  Also, we now
	allow V4 through V6 terms in force-field substructures.

	Extra options have been added to the EXNB command to allow
	placement of all nonbonded pairs on the pairlist;  this also
	bypasses pairlist updates during energetic simulations.  This
	feature should be useful when studying small or medium-size
	molecules with GBSA solvation.

	The FXTA command has been enhanced to allow the specification
	of multiple flat-bottom constraints for the same torsion.  This
	facilitates modeling in the context of constraints dictated
	by NMR results via the Karplus equation.

	Network-distributed BatchMin jobs no longer require a special
	startup script.

	Distributed BatchMin jobs now allow specifying which BatchMin
	executable is to be run on the remote hosts. This allows
	use of a special program version parameterized for the hardware
	in use.  A remote user account different from the local one
	may now be specified as well for each host.

	SGI distributions now include BatchMins optimized
	for the R3000 (-mips1), R4x00 (-mips2) and R8000 (-mips4)
	architectures.  IBM RISC distributions include versions
	optimized for the Power-1 (e.g., 530), Power-2 (e.g., 590)
	and PowerPC (e.g., 250) architectures.

	New, high-quality force field parameters have been
	developed from HF/6-31G* (or higher) ab initio calculations,
	and Chelp-G charges.  Force field parameters have been
	developed for 1,5 hexadiene, butane,(2-hydroxyphenyl)benzotriazole,
	proline, isopropyl and cyclopropyl carboxamide,
	methyl ethyl ether, 2-propanol and anisole, as well as
	for acetal, carbohydrate and sulfonamide systems.
	Some of the parameterizations are described in the Technical
	Manual.

XCluster:

The new command is described in the XCluster Manual.

        The Writerep: command writes out a single "representative" 
	structure for each cluster at the desired clustering level.  
	This functionality is also available from File/Write in the
	X interface.

Referencing MacroModel:

  Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.;
  Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C.

  "MacroModel-An Integrated Software System for Modeling Organic and
  Bioorganic Molecules using Molecular Mechanics"

  J. Comput. Chem. 1990, 11, 440.


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