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Index
Acknowledgements: I would like to give
special thanks to Denys Bashtovyy for directing me to some interesting websites in
molecular modeling and providing some useful comments of this website.
Online Protein
Viewers
Software Used in Molecular Modeling and Molecular Dynamics
 | AMBER (UNIX; proprietary) at Peter A. Kollman's research
group at the University of California San Francisco
(Updated 5/22/99).
 | Description: 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). |
|
| AMMP (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). |
| CHARMM 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)
| CHARMM Commands |
| Description: 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). |
|
| Chem2Pac 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
6/16/99).
|
| EGO (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). |
| GAMESS 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).
| Description: 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). |
|
| GROMACS (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). |
| MEPSIM distribution (Code obtainable through email; Website currently under
construction) for Molecular Electrostatic Potential SIMilarity Analysis
(Updated 5/22/99)
| Description: 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). |
|
| MOLGEN (MSDOS; free downloadable) automatic structure
elucidation (FTP site)(Updated
5/22/99)
| Description: This software allows the user to do various
calculations (i.e. HOMO, LUMO, potential) on small molecules (Updated 5/22/99). |
|
| MOLSCAT (UNIX;
free downloadble) is a code for quantum mechanical (coupled channel)
solution of the nonreactive molecular scattering problem (Updated 5/22/99). |
| MolScript (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).
| Documentation |
| Description: 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). |
|
| MMTK (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).
| Description: 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). |
|
| TINKER 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).
| Molda 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) |
|
| WHAT 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) |
Cool
Molecular Modeling Sites
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