Molecular Dynamic and Geometry Optimization

[CM] AMBER (Assisted Model Building with Energy Refinement) refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of this package is AMBER ver 5 which is sold for UCSF by Oxford Molecular. The code is written in Fortran and C and requires approximately 65 megabytes of disk space.
[*] New! AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features,like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP.
[*] New! AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers.
[*] New! ARTwork is a program for MD and Monte Carlo simulations based on Effective Medium Theory. The program has built-in interaction potentials based on the effective medium theory (EMT). Alternatively, the user can supply an external program for calculation of the interactions and still take advantage of the setup, dynamics and analysis facilities. The EMT potential that comes with the program allows calculations of Cu, Ag, Au, Ni, Pd, Pt and their alloys and the interaction of oxygen and hydrogen with these metals. The potentials are approximate, but despite their simplicity, they have been shown capable of describing a large number of bulk and surface properties of metals and chemisorption systems very well.
[*] AutoDock is a suite of programs designed to predict the bound conformations of a flexible ligand to a macromolecular target of known structure, like an enzyme or nucleic acid. AutoDock has also been used in the prediction of the structure of protein-protein complexes. AutoDock has found application in the computer-aided design of bioactive compounds and in the prediction of peptide binding to antibodies. Free only for academics.
[*] Biomer is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics.
[*] BOSS (Biochemical and Organic Simulation System) performs (a) molecular mechanics energy minimizations, normal mode analysis, and conformational searching with the AMBER/OPLS force fields, and (b) Monte Carlo statistical mechanics simulations for pure liquids and solutions of zero to 25 solute molecules in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase.
For more information contact: Prof. William L. Jorgensen, Department of Chemistry, Yale University, P. O. Box 208107, New Haven, CT 06520-8107 USA. Tel: + 1 203 432 6278, Fax: + 1 203 432 6299, E-mail: bill@adrik.chem.yale.edu.
[*] BRAGI is a interactive protein-modelling program. It was developed for the special purpose to model unknown proteins from the structure of a known one. But it has many other possibilities:
  • Display of proteins or non-proteins; Different file formats (Brookhaven, RDI, Sybyl MOL2)
  • Display of structures in various modes (space filling, Ball&Stick, tube, ...)
  • Display in stereo mode
  • Calculation and display of the molecular surface (coloured by electrostatics or hydrophobicity; solid or wireframe)
  • Calculation and display of secondary structure
  • Display of backbone torsion angles (RAMACHANDRAN-Plot)
  • Exchange of amino acids & variation of torsion angles with interactive energy calculation
  • Comparison of the three dimensional structure and supercomposition of two molecules by RMS fitting
  • Calculation of covalent and potential hydrogen bonds
  • Output as a hard copy or plot
  • Building or replacing protein loops
  • Creation of new or variation of molecules in a molecule editor (still in development)
[GPL] BTL (Bioinformatics Template Library) uses templates to implement generic programming in same way as the Standard Template Library (STL). The focus of this library is on the data structures and algorithms used within the fields of bioinformatics and molecular modelling. This library uses templates to implement generic programming. Templates allow the development of efficient generic programming modules using compile-time mechanisms. Although the BTL has been designed with biomolecular applications in mind it contains classes of more general utility.
[*] CHARMM (Chemistry at HARvard Molecular Mechanics). Features contributed include a good deal of the parallel processor support, rigorous constant pressure and Ewald summation methods, X11 and Postscript graphics support, and an interface to GAMESS for ab initio based QM/MM simulations. The lab has also been exploiting high speed networking to achieve parallel computing systems at comparatively low cost (LoBoS).
[*] Distance Geometry Ask to Thomas Huber by mail to have a running C version of DGEOM 95. (The original fortran file could not be compiled with f2c/gcc). Contact QCPE for the DGEOM license.
[*] DL_POLY is a parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Advanced Research Computing Group (ARCG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.
[*] DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together. Compounds which dock to each other well, like pieces of a three-dimensional jigsaw puzzle, have the potential to bind, and compounds which bind to biological macromolecules are candidates to act as drugs (Free for academics).
[*] DPMTA (Distributed Parallel Multipole Tree Algorithm) is a portable implementation of the Paralel Multipole Tree Algorithm (PMTA) which runs in a distributed environment under the PVM toolset. DPMTA provides application programmers with a easy to use interface to compute full N-body interaction solutions. Although DPMTA is targeted mainly for the high precision requirements of Molecular Dynamics (MD) simulations, its generic interface makes it useful for many other applications. DPMTA has been successfully incorporated into several existing MD programs, including Sigma and NAMD.
[*] EGO is a program to perform molecular dynamics calculations on parallel (under PVM, MPI or PARIX) as well as on sequential computers.
The energy function employed partially derives from the one used in the program X-PLOR of A. Brunger. EGO can read X-PLOR pdb, psf, and parameter files and EGO output files can be converted to X-PLOR DCD/crd files and read back into X-PLOR for further analysis of the resulting trajectories.
[*] FANTOM (Fast Newton - Raphson Torsion Angle Minimizer): calculation of conformations of linear and cyclic polypeptides and proteins with low conformational energies including distance and dihedral angle constraints from nuclear magnetic resonance experiments or for modeling purposes. The user can run energy minimizations and/or Monte Carlo simulations of an empirical energy function. Protein-solvent interaction is included with a fast routine for the calculation of accessible surface areas of individual atoms and their gradients. FANTOM is also suited for the exploration of low energy conformations of cyclic peptides or flexible loops in proteins.
[*] gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from programs like the GaussianXX.
[*] GROMACS - Molecular Dynamics on Parallel Computers with MPI or PVM. Some features of the software:
  • Standard Molecular Dynamics simulations
  • Energy minimizations
  • NMR Refinement using NOE data
  • High performance due to well optimized code and smart algorithms
  • Automatic topology generation from a building block library
  • Flexible force field usage
  • Non-Equilibrium Molecular Dynamics
  • Many analysis tools
  • Many preprocessing tools
[*] GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold:
  • Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method.
  • Energy minimisation of arbitrary molecules.
  • Analysis of conformations obtained by experiment or by computer simulation.
[CM] ICM is a new program for molecular modeling and high-performace molecular visualization and animation in the following research areas: modeling by homology, structure predictions and analysis, flexible protein-protein and protein-ligand docking, bioinformatics, data analysis, statistics and plotting.
[*] ICMlite is the free version for academics.
[*] MDComm is a set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD. It is built on the RAPP software package (developed by Rick Kufrin at NCSA), which simplifies the process of building and maintaining interactive client/server applications. (Note: The latest MDComm library is still under development and the source code and pre-built binaries will be released once it is completed.) The programs can be used together or independently.
[*] MDScope MDScope is an integrated set of computational tools which functions as an interactive visual computing environment for the simulation and study of biopolymers. The project implements standard visualization and simulation methods and offers a foundation for testing new algorithms and capabilities.
At the core of MDScope are three major software components:
[*] MMTK (Molecular Modelling Toolkit) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling.
[*] MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible.
[GPL] Moldy is a computer program for performing molecular dynamics simulations of condense matter. It can handle any assembly of rigid polyatomic molecules, atoms or ions and any mixture therof. It uses the 'link cell' method to calculate short-range forces and the Ewald sum technique to handle long-range electrostatic forces. Simulations may be performed either in the usual NVE ensemble or in NVT (and others) ensembles using Nose-Hoover thermostat and Parrinello and Rahman constant-streee methods. As the MD cell need not be cubic, the program is equally suitable for simulations of solids and liquids. Most existing MD program are limited in their capabilities, for example to one kind of potential function, or molecular symmetry, or to some restricted number of molecules. Moldy is (as far as possible) free from such arbitrary constraints. The system is specified at the beginning of each run and its size is only limited by the amount of menory available to the program.
[*] MOPAC 7 is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. The semi-empirical Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with respect to molecular geometry. Using these results MOPAC calculates the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers. For studying chemical reactions, a transition state location routine and two transition state optimizing routines are available. It is available for Linux on this machine. There is another place where you can find MOPAC 7.
[*] NAMD (Not (just) Another Molecular Dynamics program) is a MD program designed for the simulation of large biomolecular systems on distributed memory machines. It is written in C++ in a modular fashion so that new algorithms may be readily tested. (Note: this should be fully Linux compatible, as suggested by authors of NAMD.)
[CM] PCMODEL Complete molecular model builder, conformational searching, interface to Gaussian, Gamess, TurboMole, Ampac, Mopac and more. Comes with MMX, MM3 and MMFF94 force fields. Version 7.
[*] PMD is a scalable, parallel program for the efficient simulation of the molecular dynamics of biological macromolecules. PMD utilizes the Greengard/Rokhlin Fast Multipole Algorithm to allow the simulation of very large biological macromolecular systems without sacrificing the important long-range Coulomb interactions. The force field implemented by PMD is compatible to programs such as CHARMM, X-PLOR, GROMOS, Discover and others. Residue topology and parameter files suitable for X-PLOR can be used with PMD. Particularly, PMD can fully implement the CHARMM19 CHARMM22 force fields. PMD is also intrinsically and transparently parallel and suitable for running on a wide variety of parallel architectures, both shared memory and message passing (PVM or MPI).
[*] SIgMA (SI-mulations of MA-cromolecules) is a system of programs and data files for doing Energy minimization, Free Molecular dynamics, Constrained and restrained molecular dynamics, Molecular dynamics with free-energy methods of biological macromolecules. Using Sigma one can work with periodic boundary conditions and simulate molecules in solvent water. (In principle, Sigma can also handle the more complex periodicity of crystals. However, the currently running fast version of Sigma cannot handle any except orthogonal P1 "symmetry".)
[*] SOLVATE is a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. SOLVATE generates irregularly-shaped solvent volumes, adapted to a given solute's structure, allows efficient computation of boundary forces as required in molecular dynamics simulations, and guarantees a minimal solute-boundary-distance, It also guarantees a minimal solute-boundary-distance, generates `disordered' (= fluid) water, not a grid of water molecules (= ice), and locally minimizes the positions of all water molecules.
[*] TINKER (molecular modeling software) is a complete package for molecular mechanics and dynamics of molecules, especially polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER/OPLS, CHARMM22, MM2(91), MM3(96), AMBER-95, OPLS All-Atom, ENCAD, MMFF-94 (in progress) and our own TINKER set. It also implements a variety of novel algorithms such as: a new distance geometry metrization method that is faster than standard algorithms, Elber's reaction path methods, diffusion equation and density annealing global optimization via potential smoothing, multipole expansion treatment of electrostatics and polarizability, Eisenberg-McLachlan ASP and Macromodel GB/SA solvation, our own truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, a new spherical energy cutoff method, reaction field treatment of long range electrostatics, and much more....
[*] Understanding Molecular Simulation From the Preface: "The book is aimed at readers who are active in computer simulation, or are planning to become so. Computer simulators are continuously confronted with questions concerning the choice of technique, because there is a bewildering variety of computational tools available. We believe that, in order to make a rational choice, a good understanding of the physics behind each technique is essential. Our aim is to provide the reader with this background." FORTRAN source code is available for some examples.
[*] VMD (Visual Molecular Dynamics) is a program for interative display and animation of molecules. It runs on SGI, Sun, HP, IBM, and Linux workstations. It supports OpenGL and Iris GL accelerated 3-D rendering. VMD can be compiled from source for all supported platforms. Binaries are currently distributed for SGI, Sun, HP, and Linux. The program is a part of MDScope, (see Molecular).
[*] WinMGM is a molecular graphism program. It allow to display and manipulate one or more molecules. You can add ribbons, solvent accessible surface, hydrophobic/electrostatic/custom isopotentials..., use various display modes. A full screen mode, faster, is also available. A separate command line program, optimgm2, allow to do energy optimisation (Monte-Carlo, systematic analysis, simplex) and peptide construction.