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.

Ghemical은 C++로 작성된 계산 화학 소프트웨어 패키지입니다. Ghemical은 그래 피컬 사용자 인터페이스를 가지고 있으며, 양자 역학 (반경험적) 모델과 분자 역 학 모델 양쪽을 모두 지원합니다. 구조 최적화, 분자 동력학 그리고 OpenGL을 사 용하는 여러가지 시각화 도구등이 현재 사용할 수 있습니다.

Ghemical은 양자 역학 계산을 제공하는 외부 코드에 의존합니다. 반경험적 방법 MNDO, MINDO/3, AM1 그리고 PM3은 MoPAC7 (퍼블릭 도메인)패키지에서 가져왔으 며, 이 패키지에 포함되어 있습니다. MPQC 패키지는 순이론 방법을 제공하기 위 해서 사용되고 있습니다: Hartree-Fock 이론에 근거한 이 방법은 현재 STO-3G 에 서 6-31G** 까지 범위를 기본 세트로 함께 지원됩니다.

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.