When I test or run DOCK with the amber_score, I get something like the following error:
cd test/amber_score_1lgu ; make move_ligand.dockout Reading parm file (1lgu.lig.1.prmtop) title: getpdb: can't open file lig.1.amber.pdb make: *** [move_everything.dockout] Error 1
What is causing the error and how do I fix it?
Known causes are an incorrectly defined AMBERHOME environment variable and a correctly defined AMBERHOME environment variable that points to a faulty AMBER installation. The problem is that one of the steps of the amber preparation scripts is failing. The error is buried inside one of the amberize_bla.out files. The simplest patch is to undefine AMBERHOME; the amber preparation scripts will then use the default DOCK supplied AMBER programs. A possible cause is a faulty DOCK installation; surprisingly, this cause has not been reported.