Author: Andy Good, Daniel Gschwend
autoMS is an extremely useful tool for setting up for sphgen . This script converts PDB files to QCPE ms input format, runs a QCPE ms surface calculation, converts the resulting surface to UCSF MS format with reformatms , creates a SYBYL dot file of the surface (if ms2dot is available), and prepares an 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.
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