Note: Software Database is still being populated.
Software / Molecular Dynamics | |
| Amber Version(s): 1 | Support: None "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. | |
| APBS (Adaptive Poisson-Boltzmann Solver) Version(s): 1 | Support: None APBS: Adaptive Poisson-Boltzmann Solver Software for evaluating the electrostatic properties of nanoscale biomolecular systems APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules, * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. | |
| charmm Version(s): 2 | Support: None CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. NOTE: Our CHARMM installation uses a CHARMM license issued by Martin Karplus and Harvard University, which is a for money license issued to me; it is not a site license. If you have your own license of CHARMM please contact biohelp@ittc.ku.edu and access will be granted to the versions of CHARMM installed. | |
| GROMACS Version(s): 2 | Support: None GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Machine(s):
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| mdenergy Version(s): 1 | Support: None MDEnergy is a program to calculate energies from DCD or PDB-files. It is originally derived from Mindy, a simplified version of the NAMD engine, written by Justin Gullingsrud. It can calculate the different bonded and nonbonded energies for each atom based on the information from the PSF-file and the coordinate file that you have to specify. The total energy values are identical to the NAMD output, except for roundoff errors in case you specify the same cutoff and switch distance as in the NAMD input file. You can also compute the energy for a selection of atoms or determine the interaction energy between two sets of atoms. MDEnergy is very memory efficient because is processes DCD files frame by frame. The output format is similar to NAMD's output and you can plot it with 'namdplot' (comes with NAMD). | |
| namd Version(s): 1 | Support: None NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. Machine(s):
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| pdb2pgr Version(s): 1 | Support: None PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields PDB2PQR was ported to Python by Todd Dolinsky while working with Nathan Baker at Washington University in St. Louis. The PDB2PQR code is based on C++ design and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to facilitate structure preparation for APBS. PDB2PQR uses PROPKA to determine protein pKa values. PROPKA is developed by the Jensen Research Group at the University of Copenhagen. More information about PROPKA can be found at http://propka.ki.ku.dk/. PEOE_PB charges for ligand parameterization were developed by Paul Czodrowski in the Klebe Group at the Philipps University Marburg. | |
| xplor Version(s): 2 | Support: None Machine(s):
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