[qNq]

Let me to introduce a program of molecular modeling "Abalone".
http://www.biomolecular-modeling.com/Abalone/index.html



The main features are:

•     Molecular graphics
•     Molecular model building
•     Geometry optimization
•     Molecular dynamics simulations
•     Hybrid Monte Carlo
•     Implicit and explicit water models

Much attention is paid to design the initial models. There is a constructor of chain molecules, which allows to create a model with pre-installed molecular-mechanical parameters form the residues. Users can create their own residues and add them to the database. There is a procedure for adding the box with a solvent, such as a water. This box should be made separately and then added to the model. The overlapping solvent molecules can be automatically removed.