VeraChem - Version VMap 0.9 - Small Molecule Tools - Manual

Superimpose related ligand series on reference structure Reference can be co-xtal PDB, sdf, mol, crd Handles arbitrary atom orderings. Provides excellent VM2/docking starting structures. VMap is an  application to superimpose related ligands (e.g. common scaffold atoms; different R-groups) on a reference molecule. The reference can be, for example, a co-crystalized ligand taken from a protein PDB file, in which case, VMap provides excellent starting structures for VM2 or docking calculations.