While running docking of indomethacin with a receptor, Autodock4 doesn't work. In the DLG file, it was stated that the Cl.map file is not found. How can I resolve this problem?
First, try to recalculate the grid maps with AutoGrid4. It should solve your problem.
If the first step doesn't work, while defining map types (Set Map Types option) there should be an atom list like "A C HD N ...". Add the missing atom here manually and calculate grid again. That will produce the missing map there.
P.S. You can also do this by adding the missing atom in the grid paramater file(.gpf)
Sometimes during preparation this problem occurs that Autogrid does not create all files....so delete all files prepared by Autogrid and rerun. Also, make sure the filename is not too big.