On Fri, Jan 09, 2004 at 06:34:14PM +0100, Antoine Leimgruber wrote: > I use this kind of commands in my top files. > > SET DIRECTORY = 'path_to_topfile' > SET ATOM_FILES_DIRECTORY = 'path_to_topfile' > SET OUTPUT_DIRECTORY = 'path_to_topfile' > > However, all the *.V* files are generated in the directory where the > perl script launching modeller is and not in the directory where the > top file actually is. > What is the equivalent for these files ? Unfortunately, all energy profiles (including violations) get written to the current directory, ignoring OUTPUT_DIRECTORY, so there's nothing you can do about this other than try to work around it. This is a bug in Modeller, which will be fixed in the next release. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage