Molecular modeling software (2013)

Complete solutions

An environment for molecular modeling must include: GUI environment for all its subprograms, tools for creating and editing molecular and crystal structures, subprograms performing electronic structure calculations (semiempirical and ab-initio, crystals and molecules), subprograms performing molecular dynamics simulations (classical and quantum), other subprograms calculating some specific quantities, and finally tools for visualizing and exploring the results of computations. All such environments known to me are commercial. Some of them have student licenses: Spartan 14 ($50), HyperChem 8 ($80).

File formats

Currently there is no a versatile commonly accepted chemical file format for storing both molecular and crystal structures.

• The standard file format for storing crystal structures is CIF (Crystallographic Information File, see Core CIF Dictionary). See a template.
• One of the most universal format is PDB (Protein Data Bank, the same as ENT), but its fixed precision (8.3) format impedes its use for storing coordinates optimized by quantum chemistry calculations. See notes on editing pdb files and examples of pdb files in the present site. See a template.
• The simplest format is XYZ containing only atom names and cartesian coordinates. See a template.
• See also SMILES format and its online translator.
• Different formats can be converted by Open Babel 2.3.2 program.

Viewers

• Jmol 13 (open-source) – molecules and crystals. In addition it renders surfaces and has a powerful scripting language. Observed limitations: very limited customization, poor tools for visualizing crystals.
• Mercury 2.4 (free version) – molecules and crystals. Observed limitations: rendering is either slow with "-nodirectrendering" option or corrupted without it (Windows 7), most of the elements are rendered by the same color and the implemented use of style sets is inconvenient, coloring by symmetry works only for molecular crystals.
• Diamond 3.2 (expensive, demo version) – editing and analyzing crystal structures. Observed limitations: does not recognize some PDB files and space groups in some settings, e.g. P2₁/n.