Open Source Chemistry Software

A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.

Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html

ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations", J. Chem. Theory Comput. 11 (2015), 2517-2524 L.C.Kröger, W.A.Kopp, M.Döntgen, K.Leonhard, "Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations", J. Chem. Theory Comput. 13 (2017), 3955-3960 M.Döntgen, F.Schmalz, W.A.Kopp, L.C.Kröger, K.Leonhard, "Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations", J. Chem. Inf. Model. 58 (2018), 1343-1355 Check the Wiki for bug reports and fixes.

An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges

This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

Solve four different cubic equations of state to obtain three roots of molar volume at a given temperature and pressure. These four cubic EoS are :- 1 Van der Waals equation of state 2 Redlich–Kwong equation of state 3 Soave modification of Redlich–Kwong 4 Peng–Robinson equation of state

The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations.

Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome to post any bug or request under BUGS & REQUESTS menu. (sourceforge account will be needed).

Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring-chain tautomerism. MolTPC provides an adjustable and fully automatic approach for this problem. The original publication can be found on http://onlinelibrary.wiley.com/doi/10.1002/jcc.23397/full.

This is a general open source Quantum Mechanics/Molecular Mechanics project with academic origin. Its intention is to produce free software tools to study molecular systems through QM/MM, in open collaboration.

ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator of molecule-water complexes with graphical user interface (GUI), 2) semi-automatic frequency analysis using symbolic potential energy distribution matrix and comparison of optimized internal coordinates, 3) GUI for charge fitting with three modes: manual, Monte-Carlo sampling or brute force, and 4) GUI for dihedral terms fitting. The usage of these tools decreases the labor effort, lowers manual input errors and reduces the time needed for accurate MM parameterization efforts.

chemkit is an open source software library for chemistry applications, particularly in the areas of cheminformatics, molecular visualization and molecular modeling.

MDcore is an Open-Source library implementing the core functionality of a Molecular Dynamics engine. The engine is inherently multi-threaded and runs efficiently on multi-processor/multi-core shared-memory architectures.