Required Parameters

-target <filename>
-protein <filename>
-p <filename>

[keyless parameter 1]

The format must be one that retains partial charges: OEBinary, Tripos .mol2, or DelPhi flavor PDB (where there is radii in the occupancy field and charge in the B-factor field).

The file format of the input file is automatically determined from the file extension. The extensions .oeb, .oeb.gz can be OEBinary; .oedu for OEDesignUnit; *.mol2 for Tripos Mol2 files; .pdb for PDB format files.

File type





.oeb .oeb.gz


.pdb .ent .pdb.gz .ent.gz


.mol2 .mol2.gz


By default, charges and radii are expected to be in this file and the results will be meaningless if they are missing. The program SPRUCE is provided to prepare the biomolecular structure including assigning charges and radii.

Atoms from waters, metals, ligands, co-factors, modified proteins and nucleic acids will be included in the calculation, except when using an OEDesignUnit, in which case only the protein and nucleic acid content will be used. VIDA can be used to create a new molecule where the protein is split from these.