INSPH file for running sphgen. The
requirements are only two files: a receptor PDB file, and an exclude.pdb file.
The exclude.pdb file is a subset of the receptor and contains the residues
which should not be surfaced in the MS calculation. This file can be created
in several ways. The easiest, if SYBYL is available, is to select all residues
in the receptor within some radius of a known ligand, invert the selection, and
write out the file in Brookhaven format as exclude.pdb. One alternative that
does not require SYBYL is to use get_near_res to locate all receptor
atoms or residues within a specified radius of a known ligand and invert the
resulting pdb file using invertPDB.
Usage: autoMS receptor_PDB_file [surface_density] [probe_radius]
where surface_density and probe_radius are optional, defaulting to 3.0 dots/Å2 and 1.4Å, respectively. Note: before using the first time, the directory specification for the DOCK hierarchy must be updated inside the autoMS script.