ap_docking_crmsd calculates crmsd between ligand positions after flexible docking to a receptor and a reference.
The program reads in a native pose and at least one PDB file with a computed pose (i.e. a model), each of them must contain a ligand molecule bound to a protein receptor. The ligand can be a small molecule, peptide or even a protein. The program finds the ligand either by residue ID (a three-letter code, such as CAM) or a chain ID - a single letter code.
USAGE: ap_docking_crmsd 2m56-ref.pdb CAM 00199.pdb 00963.pdb 04473.pdb ap_docking_crmsd 2m56-ref.pdb X 00199.pdb 00963.pdb 04473.pdb ap_docking_crmsd - X 00199.pdb 00963.pdb 04473.pdb
where 2m56-ref.pdb is the native and CAM is the three-letter PDB code of the ligand for which crmsd will be evaluated and 00199.pdb and the two other files are conformation after docking. In the second example, X is the ID of the chain containing a ligand molecule.
The program evaluates crmsd based on ligand cooridinates upon an optimal superimposition of a receptor between the refence and any model of any input file. If the reference structure is not given and dash ‘-‘ character is used instead (as in the last example), the program evaluates pairwise all-vs-all crmsd calculations