Input Preparation

Ligand Preparation

The most common use of POSIT is to dock molecules into the active site of a target protein. For the purposes of this document, we’ll call the file(s) of molecules the database file(s), or dbase file(s). The most common format for database file(s) is a multi-conformer OEBinary file created by OpenEye’s OMEGA program, however, this file can be one of several 3D formats. These formats include SDF, MOL2 and PDB. POSIT determines the database file format from the file extension, .sdf or .mol for SDF, .mol2 for MOL2, .pdb or .ent for PDB. Gzip compressed files of these same formats are allowed as well. POSIT will interpret infile.sdf.gz as a gzip’ed SDF file.


Note that even though all these formats are supported, using SDF, PDB or MOL2 can result in a loss of speed due to the I/O penalty of these formats.

POSIT internally generates 3D conformations OMEGA if a 1D/2D molecule is supplied.

By default POSIT will interpret conformers in the database file(s) as part of a single multi-conformer molecule as long as they:

  • Are contiguous in the input file.
  • Have the same numbers of atoms and bonds in the same order
  • Have identical atom and bond properties with their order correspondent in the subsequent connection table
  • Have the same atom and bond stereochemistry

While this may appear to be a restrictive list, many programs write multi-conformer molecules into SDF or MOL2 files such that the above rules will be satisfied. If the conformers are named differently, (i.e. they have a conformer number appended to the base name like acetsali_1, acetsali_2), POSIT will still consider them part of a single multi-conformer molecule if the criteria above are met.

Receptor Preparation

POSIT can use either a single receptor or multiple receptors each of which contains a different structure/conformation of the target protein. Each receptor must also have a bound ligand. Receptors with bound ligands can be created with the following programs.

Program Type Description
MakeReceptor GUI Interactive GUI for creating a receptor.
Spruce4Docking Command Line Prepare and creates receptor(s) from a PDB or MMCIF file, contaning a protein-ligand complex.
DU2Receptor Command Line Convert a prepared OEDesignUnit file to a receptor


Receptors can also be created using the Docking Toolkit (see the Docking Toolkit documentation).