Before starting the stimulation part of molecular modeling (such as molecular dynamics), one should have a fully assembled and optimized initial molecular model. Our program support such model construction.
Chain molecule assembly
Most large molecules explored by chemists and biologists are chain structures composed of residues of one or several types. It is recommended to assemble such molecules using the chain builder. It is not just convenient; essentially, the residues manipulated by the builder include atoms with specified molecular mechanics types. Their correct specification is not a trivial task. This makes the chain builder a basic tool to construct molecules.
Merging models from several files
Despite the task simplicity, there are several issues that make the program assistance quite valuable here.
First, atoms are numbered in many file formats. Their numbering can be consecutive, individual for each molecule, or missing. This introduces the task of renumbering, which is easy for a program and complex for a human.
Second, superposition of atoms should be avoided in model merging. If we want to add many solvent molecules to a current model, the solvent molecules substantially overlapping with the main model molecules can be removed.
Third, it is essential to be able to move models in space relative to each other. The intermediate result should be visible on screen.
Immersion in solvent
Generated models sometimes should be immersed in a box with solvent. Usually, a box with solvent is generated separately and added to the main model. The simplest way to do it is to repeatedly replicate one or several solvent molecules with a spatial shift along the three axes. This gives rise to a crystal-like structure. This structure can be used immediately or, preferably, after a rough molecular dynamics equilibration.
Abalone make it possible to measure and edit the distances, angles, and dihedral angles.
Additionally torsion angles can be specified using conformational prototypes (which are used by the chain builder, in particular). The conformational prototypes are a part of the mlm file format, which is the basic format for all our products. After some torsion angles are added to the end of the mlm file, first, the Cartesian coordinates of the atoms are set and then the torsion angles are adjusted. As a result, the atomic coordinates in the model can differ from the specified Cartesian coordinates.
Molecular geometry optimization
After a molecule is drawn, it nearly always requires to be optimized. Even if the bond lengths and valance angles were correctly specified, most likely there are problems with overlapping atoms. This problem can be solved in a few tens of optimization steps.
AMBER and OPLS are the basic force fields in the package. The force field parameters are defined in text files in the data/ForceField folder.