How do I tell AutoGrid/AutoDock where input files are?
Since AutoGrid/AutoDock look for input files in current working directory (cwd), you need to make sure that your cwd includes all input files necessary. Start your command line shell and run ls (POSIX) or dir (Windows). If the input file mentioned in error message is not listed, you need to change directory (cd) or move required input file to cwd. Please note that AutoDock is a command line application and you need to be able to navigate your file system in order to troubleshoot potential problems. See, for instance, File Systems – Unix and Dos. The above is also true if you launch AutoDock using AutoDockTools (ADT). If you changed your directory while saving or opening an input file then chances are that you need to change current working directory in ADT.
