DebiChem Molecular modelling packages

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

• Molecular modeller with automatic force-field based geometry optimization
• Molecular Mechanics including constraints and conformer searches
• Visualization of molecular orbitals and general isosurfaces
• Visualization of vibrations and plotting of vibrational spectra
• Support for crystallographic unit cells
• Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
• Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

BALLView provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

BALLView can be considered a graphical user interface on the basis of BALL (Biochemical Algorithms Library) with a focus on the most common demands of protein chemists and biophysicists in particular. It is developed in the groups of Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen, Germany). BALL is an application framework in C++ that has been specifically designed for rapid software development in Molecular Modeling and Computational Molecular Biology. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

• Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
• Molecular builder and sculptor
• Internal raytracer and movie generator
• Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations.

nMOLDYN is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.