On Thu, Aug 26, 2004 at 06:56:31PM +0530, V Nadeem Ahmad wrote: > I was trying to do modelling with hetatm .it stopped after running a > while can anyone help me where was the mistake. > > ## the top file is > > INCLUDE # Include the predefined TOP routines > SET ALNFILE = 'align.pir' , KNOWNS= '1a57', SEQUENCE = 'seq' > SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on > SET TOPOLOGY_LIBRARY = $(LIBS_LIB6V2)/top.lib > SET PARAMETERS_LIBRARY = $(LIBS_LIB6v2)/par.lib > CALL ROUTINE = 'model' # do homology modelli
Your variable names are incorrect. See http://salilab.org/modeller/FAQ6v2.html#15 and make the following substitutions:
MODEL_TOPOLOGY -> TOPOLOGY_MODEL TOPOLOGY_LIBRARY -> TOPLIB PARAMETERS_LIBRARY -> PARLIB
Ben Webb, Modeller Caretaker