Required Parameters

-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; .mol2 for Tripos Mol2 files; .pdb for PDB format files.

File type Extension
OEBinary .oeb .oeb.gz
PDB(DelPhi) .pdb .ent .pdb.gz .ent.gz
MOL2 .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 SZMAP is provided to add charges.

Atoms from waters, metals, ligands, co-factors, modified proteins and nucleic acids will be included in the calculation. VIDA can be used to create a new molecule where the protein is split from these.