The Modeling Facility has a site license for MacroModel, a package for molecular mechanics and conformational searching of organic and biomolecules. The latest version is 8.1. This version only works on model1-6, & 8 and does not work on SGI Indigo2 machines. If you want to use version 8.1 you need to type (in a csh or tcsh shell):
>maestro (or macromodel81)
then to run the program type
*Note that the "macromodel" graphical interface is not available in version 8.1; everything is done through maestro. The version 8 license is a floating license and should run on any subnet up to the maximum of 16 users (Batchmin jobs). Theoretically, an unlimited number of users can use the maestro GUI at one time.
To use MacroModel version 7.1 in the Modeling Facility, type:
>macromodel (or macromodel71)
*Temporary licenses are available to run 7.1 from
two subnets in Natural Sciences I (128.200.228.* and 128.200.229.*).
These temporary licenses will be in effect until 2/15/03. Maestro license for MacroModel v7.1 expires on 2/15/03. The"macromodel" graphical interface will be available to run macromodel version 7.1.
To use MacroModel version 6.5, type:
The new graphical user interface for MacroModel is called Maestro. Maestro will only work on model1-6. To use this GUI, type:
Description of MacroModel
MacroModel Home Page
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MacroModel structures are stored as atom connection tables with Cartesian atomic coordinates. They may be created by the user or generated from Brookhaven Protein Databank files. Tools are provided for graphical drawing, substructure/residue replacements, fusions and connections. An automated 3D structure growing method facilitates structure building for biopolymers (peptides, nucleic acids and carbohydrates) in a number of standard conformations. All selections can be used for de novo structural input or for modification of existing structures. Geometry modifications are achieved using tools for angle and torsion angle rotation, chiral center inversions and double bond inversions. On GL-equipped workstations real-time independent molecular translation/rotation with distance and angle monitors and variable sensitivity "bump-checking" allows bimolecular docking. Hydrogens can be added to entire structures automatically to complete the valence of atoms in the structure.
MacroModel's energy calculations are performed by the BatchMin program. Multiple simultaneous energy calculations can be initiated from a MacroModel session. BatchMin tasks (even those on a remote computer) can be interactively monitored, disconnected from and reconnected to. Energy calculations are performed by molecular mechanics using a user-specified force field. We supply the MM2*, MM3*, AMBER* and OPLSA*, AMBER94 and MMFF (Merck-Molecular) force fields. The force field parameters are supplied in ASCII form, and may be modified by the user to accommodate special molecular structures.
Rapid, highly optimized full structure or substructure minimizations are available using analytical first and second derivatives. Convergence criteria are user specified and can be based on gradient, energy stabilization or atomic movement. Minimum testing by eigenvalue calculation distinguishes true minima from saddle-points and provides vibrational frequencies. Detailed listing of energetic components are available. The following geometry optimization procedures may be used:
The MacroModel implementation of the leap-frog variant of velocity Verlet integrator allows a timestep of 1.5 fs at 300 deg K with either molecular dynamics or stochastic dynamics. Initial velocity distributions can be set by temperature and positive or negative temperature variations during the simulations may be used to perform simulated annealing. Monitoring may be performed by structure sampling at regular intervals and atomic surface areas, distances, angles, torsions and hydrogen bond populations may be monitored during the simulations. MacroModel can display structures sampled during a molecular dynamics simulation as an animated movie. Translational and rotational momentum may be zeroed during the simulation and support for the SHAKE algorithm for all bonds to hydrogen and lone pairs or all bonds is included.
In addition to conventional molecular dynamics simulations BatchMin can perform mixed-mode Monte Carlo - stochastic dynamics simulations. These allow convergence to be obtained rapidly, even for systems which are flexible and have high potential energy barriers between conformations. Monte Carlo simulations in torsional space are also possible.
Powerful algorithms for global conformational searching are implemented in the MacroModel package. These allow efficient searching of conformational space defined in terms of either torsion angles (for both cyclic and acyclic systems) and multi-molecular translation/rotation. Substructure conformational searching is possible with macromolecules (e.g. protein loop searches) and molecular complexes. A single conformational search can be distributed over a number of workstations resulting in a high efficiency (greater than 80% efficient) parallel search.
This feature allows rotational energy profiles (one angle) and Ramachandran- type plots (two angles) to be obtained with full energy minimization at each constrained set of angle values. Contour plots from two-angle driving can be displayed in MacroModel.
The GB/SA continuum solvation treatment is implemented in MacroModel. This solvation model is based on a continuum dielectric for solvent polarization and solvent-accessible surface area treatment of the cavity and Van der Waals solvation components. It can be applied to molecular dynamics, conformational searching and energy minimizations and these will proceed at 25-30% the speed of calculations in vacuo. Solvation parameters are currently supplied for chloroform and water models.
An interactive tool is provided for rapid definition of substructure and constraint shells. Substructures can be used for all energy calculations including energy minimizations, conformational searches and molecular dynamics.
The user may apply variably-weighted constraints of nuclear position, internuclear distances, angles and torsions. Distance and angle torsion constraints can be set with a variable width flat-bottom well which ranges within the specified limits without energetic penalty.
MacroModel force fields are supplied as external text files for easy parameter modification or addition. An atom-based force field parameter loading system allows any molecule to be processed correctly without the need for residue name assignments. The special substructure section of the force field allows ready addition of complex substructures (aromatic systems, amino acids, etc.) to which special parameters are to be applied. The parameter referencing feature lists the source of each parameter used in an energy calculation and the confidence which has been assigned to its value. Alternate parameter sets within a specified force field (e.g. MM2 and MM2') may be easily selected and new alternate sets may be added to the force field. The force fields currently supplied are MM2*, MM3*, AMBER* (united and all atom models) and OPLSA*.
*The MacroModel implementations of these force fields may differ from those of the original authors. In particular, the MM3* force field is a modification of the original MM3 force field available in the public domain. MM3 is a registered trademark of Professor Norman L. Allinger author of the MM3 program, which is available from Tripos, Inc. and Quantum Chemistry Program Exchange.
Graphical display of internuclear distances, angles and dihedrals. Displays are updated in real-time as geometrical modifications are made. Atoms and residues can be identified by type or number using graphical selection. Automatic searching and display of possible hydrogen bonds is supported.
Least squares bimolecular superimpositions can be performed by either rigid or flexible dihedral angle fit.
Molecular volumes can be computed and displayed. Included and excluded volumes can be calculated and Boolean operations can be performed on volume elements.
In MacroModel the concept of sets is used to apply operations such as atom deletion, coloring, etc. to only a user-defined part of a structure. Sets of atoms can be defined by atom numbers, types, residues numbers or types, atom or residue sequences, atom proximity or by graphically selecting atoms, residues or molecules. AND, OR, NOT and XOR Boolean operations are supported for atom sets and provide a way for the user to select complicated subsets of atoms.
Atoms may be color-coded by atom type, residue type, hydrophobicity, charge or any user selected color. Atom coloring can be applied to a full structure or a set of atoms.
Variable radius Van der Waals and solvent accessible surfaces can be calculated and displayed as dot surfaces. Surfaces may be colored independently of the atom color on both full structures or substructures.
CPK-like models, ball and stick or "polytube" representations may be produced on GL equipped workstations. All features including rotation and substructure transformations (torsion angle variations, docking) are fully operative with space-filling model displays.
Nuclear magnetic resonance coupling constant calculations can be performed using a number of standard equations and parameter sets. The database supplied includes the Altona equation and standard equations for peptides and allylic systems. New calculations may be added by editing the text file data base.
A filtering tool provides the ability to select structures meeting user-defined geometrical criteria from a file of multiple conformations. Histogram and line plots allow the user to analyze the distribution of the constraints (interatomic distances, angles, torsion angles and energies) in the file. Tables of data for the constraints in the file can also be produced.
The XCluster program can be used to locate clusters of geometrically similar conformations in an ensemble of chemical conformations, such as a dynamics trajectory or the output of a conformational search. Clustering is performed in a hierarchical fashion, based on a choice from among several measures of difference between conformations.
XCluster is a stand-alone program, but communicates with MacroModel to allow interactive specification of the atoms or torsions to be considered in the clustering process. XCluster displays graphical representations of the interconformational distance matrix, the clustering hierarchy and various clustering statistics. These can be used together to infer the presence or absence of significant clustering. XCluster can also write files of the clustered conformations, optimally superimposed and colored, for viewing in MacroModel.
The following is a visual representation of the interconformational distance matrix from an XCluster analysis of the ring geometries in 192 roseotoxin-B conformations derived from a conformational search. The two large on-diagonal bluish blocks represent two clusters of conformations. The smaller, darker on-diagonal blocks indicate subclustering. To see how the conformations in the two main clusters differ, see the description of new XCluster features in the 5.0 version of MacroModel.
A number of manuals are supplied which describe the detailed workings of all the programs in the package and provide a tutorial for common operations. In addition to the printed manuals an on-line help system is available which provides context-sensitive help for all program operations.
MacroModel is currently parameterized to handle display of structures containing up to 10,000 atoms. A number of different versions of BatchMin are supplied allowing energy calculations for up to 5,000 atoms depending on the memory capabilities of the machine.
The following is required for running MacroModel 5.0 on an IBM RS/6000 workstation:
Optional for Force Field Viewer:
NOTE: The following libraries are included on your media when you receive MacroModel. Thus, you do not have to purchase them as they come with Macromodel
Please note that as of AIX 4.1 the Sabine board is no longer supported.
The following is required for running MacroModel 5.0 on a Silicon Graphics workstation:
Many MacroModel users find that 1 GB of disk is required to accommodate the operating system, data files, MacroModel executables and swap space.
MacroModel is distributed on 1/4 inch cartridge or 4mm DAT for the SGI and on 1/4 inch cartridge or 8mm cartridge for the IBM. No other media are currently available.
How to get MacroModel