Thursday, January 09, 2014

Software Used in Molecular Modeling and Molecular Dynamics

Software Used in Molecular Modeling and Molecular Dynamics
bulletAMBER (UNIX; proprietary) at Peter A. Kollman's research group at the University of California San Francisco (Updated 5/22/99).
bulletDescription: AMBER 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.(Updated 5/22/99).
bulletAMMP (Unix, Linux, and PC; Free Downloadable Software) 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. This software is found at Structural Biology at Jefferson and the Kimmel Cancer Center (Updated 5/22/99).
bulletCHARMM Homepage (UNIX; License Required) by Martin Karplus's group at Harvard University. Charmm has been integrated into the popular molecular modeling software package, QUANTA, of Molecular Simulations Inc. (MSI)(Updated 5/22/99)
bulletCHARMM Commands 
bulletDescription: CHARMm combines standard minimization and dynamics capabilities with expert features including free energy perturbation (FEP), correlation analysis and combined quantum and molecular mechanics (QM/MM) methods. Simulations provide insight into molecular-level structure, interactions, and energetics (Updatd 5/22/99).
bulletChem2Pac ( Windows, Free )is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files (Updated 7/14/99).
bulletmore information
bullet Dalton Quantum Chemistry Programnew.GIF (Unix and Windows; Free, but License Required)(represents a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations (Updated 7/14/99).
bulletDeep Viewer  new.GIF(free for PC and Macintosh) is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface (Updated 3/25/01).
bulletDeep Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletDomainFinder 1.0new.GIF (Free only UNIX; Linux) is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes ease of use: a state-of-the-art graphical user interface export of results for visualization and further analysis (VRML, PDB, and MMTK object format) (Updated 6/14/99).
bulletEGO (Unix and PC (with GNU-c compiler); free downloadable)is a program to perform molecular dynamics simulations on parallel as well as on sequential computers at Bayerish Acadamie of Science, Munich, Germany (Updated 5/22/99).
bulletFTDock, RPScore and MultiDock
bulletGAMESS Home Page (Unix, VMS, MVS, VM, Mac, or PC; free downloadable Software) for doing ab initio calculations at Ames Laboratory/Iowa State University (Updated 5/22/99).
bulletDescription: GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these (Updated 5/22/99).
bulletGROMACS (Unix, and PC (in the future), free downloadable for non-commercial users) is a useful suite of molecular modeling utilities available at Chemistry department University of Groningen (Updated 5/22/99).
bulletGROMOS (GROningen MOlecular Simulation) new.GIF (3043 bytes)(free for academic usage; Unix?) is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.  The site is maintained at ETH(Updated 7/17/99).
bulletMEPSIM distribution (Code obtainable through email; Website currently under construction) for Molecular Electrostatic Potential SIMilarity Analysis (Updated 5/22/99)
bulletDescription: New features of the program will include the possibility of performing GAMESS and GRID calculations within the package, taking profit of the MEPSIM modules (Updated 5/22/99).
bulletMOLGEN (MSDOS; free downloadable) automatic structure elucidation (FTP site)(Updated 5/22/99)
bulletDescription: This software allows the user to do various calculations (i.e. HOMO, LUMO, potential) on small molecules (Updated 5/22/99).
bulletMOLSCAT (UNIX; free downloadble) is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem (Updated 5/22/99).
bulletMolScript (UNIX; free for non-profit, but license required) Official Homepage by Avatar Software AB, who develops, markets and distributes software for structural biology, protein NMR and bioinformatics (Updated 5/22/99).
bulletDescription: MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually,
but not exclusively, protein structures (Updated 5/22/99).
bulletMolecular Structure Editornew.GIF with the complete source code in C and x86 assembler language and can rotate a molecule of 5000 atoms drawn with nice realistically looking balls and sticks on a lowly 80386/16MHz and can be configured to read output files generated by almost any popular quantum-chemical application (Updated 6/14/99).
bulletMMTK (UNIX (Requires Python); free downloadable) Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications at Theoretical biophysics at the CBM (Updated 5/22/99).
bulletDescription: MMTK provides researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling (Updated 5/22/99).
bulletMOE (UNIX and Windows, proprietary)  the Molecular Operating Environment is the next generation of chemical computing software. MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package (Updated 5/13/01).
bulletNAMD Home Page (UNIX; free downloadable, but registration required ) is a parallel, object-oriented molecular dynamics code designed for high- performance simulation of large biomolecular systems at the Theoretical Biophysics Group of University of Illinois at Urbana. (Updated 5/22/99)
bullet SCWRL - Sidechain placement With a Rotamer Librarynew.GIF  ( Unix; free for academic users ) is a program for adding sidechains to a protein backbone based on the backbone-dependent rotamer library. The library provides lists of chi1-chi2-chi3-chi4 values and their relative probabilities for residues at given phi-psi values, and explores these conformations to minimize sidechain-backbone clashes and sidechain-sidechain clashes (Updated 9/23/99).
bulletSwiss PDB Viewer  new.GIF(free for PC and Macintosh) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface (Updated 3/25/01).
bulletSwiss PDB Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletTINKER Molecular Modeling Package, (PC; free downloadable) it is a program that accepts a variety of different parameter files from a variety of different molecular dynamics packages, including AMBER, and CHARMM (Note: Trouble connecting to server 5/22/99, Updated 5/22/99).
bulletMolda is a Graphics interface for Tinker.  Note: the Tinker server is sometimes down, so in the near future I will try to make copies available to this site. (Updated 5/22/99)
bulletViewmol (Unix; free downloadable) is a graphical front end for computational chemistry programs.  It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.  The program has many features. (Updated 7/15/99)
bulletNAMD (Unix and Free)is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. 
bulletWHAT IF (UNIX and PC; proprietary) is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. at the EMBL Heidelberg Germany, BIOcomputing unit, 3D modeling, protein structure analysis. (Updated 5/22/99)
bulletWHAT IF (web interface) (platform independent; Free) provides nearly 2000 options in fields as diverse as
homology modeling, drug docking, electrostatics calculations, structure
validation and visualisation (Updated 6/9/99).