Software

=Software:=

Viewers and Builders:
Pcmodel, Serena Software, Kevin Gilbert will provide to class. Builder, viewer, MM, file conversion, conformational search. Jmol-builder and viewer Avogadro-builder, viewer and perhaps MM Pymol - builder, viewer and MM(?) Cactvs - builder, viewer developed at NIH

Rasmol, Swiss_prot - pdb viewers VMD - viewer for Namd code, will also do lammps Chimera -viewer and prep tool for Dock and Amber (replaces Midas) Molden - display program for Quantum chemistry output OpenBabel - file format conversion

Quantum Chemistry
Mopac ,Mopac-2009 - semi-empirical qm codes Gamess - ab initio qm code from Iowa State. MPQC - massively parallel quantum chemistry code from Los Alamos Dalton - ab initio qm code from Norway NWChem - ab initio qm code developed at PNNL

Molecular Mechanics
mengine - chembiogrid project from Indiana University Tinker - general purpose molecular mechanics program developed by Jay Ponder, Washington University

MD
GROMACS - parallel MD simulation from University of Groningen, W. van Gunsteren and H.J. Berendsen, supports multiple force fields Namd - large, parallel MD code from the University of Illinois Lammps - massively parallel MD code from Los Alamos DL-POLY - parallel MD simulation program developed at Daresbury, UK Moldy - MD simulation of condensed matter

MC
Towhee

Docking
Dock - UCSF AutoDock - Art Olsen's group at Scripps including the molecular graphics laboratory

Compilers
Gcc and gfortran are available for all Linux systems, Mac OsX, and Mingw Openwatcom.org - C, C++ and Fortran compilers for Windows Visual C - available to IU students