David Marshall wrote: > I am currently trying to model the effect of phosphorylation on a > protein. I have been kindly provided with adapted top_heav.lib and > par.lib files and I have modified restyp.lib accordingly. I have > searched the manual but cannot find commands to set these .lib files in > my .py files. I want to avoid overwriting the existing files as I do not > have access.

You presumably want to do this with the automodel class (for any other kind of modeling, you'd need to explicitly read in those .lib files anyway, so it should be obvious in that case). I just added a page to the Modeller wiki with a simple example: http://salilab.org/modeller/wiki/Using_non-standard_parameter_files

Since it is a wiki page, you can flesh out this example and add extra tips for others if you so desire.

Ben Webb, Modeller Caretaker