get_near_res

Author: Daniel Gschwend

Given a ligand PDB file and a receptor PDB file, performs either of two functions:

• Writes a PDB file containing all atoms of all residues in the receptor which have their Ca atoms within a specified distance of the ligand. A list file is also written which gives the closest Ca-to-ligand distance for each residue written.
• Writes a PDB file containing all atoms of all residues in the receptor which have any atom within a specified distance of the ligand. A list file is also written which gives the closest receptor-ligand distance for each residue written.

The list file output may be converted to an UCSF ms -i file with the condense program. This utility can also be used with the autoMS program using QCPE ms surfaces: to generate an exclude.pdb file from get_near_res output, see invertPDB .