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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)
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.