> 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 * -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: shenkin@still3.chem.columbia.edu -- Original Sender From: Address: shenkin@still3.chem.columbia.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html ========================================================================== 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. ==========================================================================