On 03/19/2010 02:04 AM, Knut J Bjuland wrote: > I used thesse commando to set toplogy information when doing an > alignment. BUt it did work when I wanted to build it. What kind of > command should I invoke to add thesse information in the build phase of > modeller. > > > env.libs.topology.read(file='$(LIB)/top_allh.lib') > env.libs.parameters.read(file='$(LIB)/par.lib')

If you want to build an all-atom model, you can just use the allhmodel class rather than automodel. It will handle everything automatically for you (it also turns on env.io.hydrogen so hydrogen atoms in your templates are read in).

Otherwise, you can assign to toplib and parlib in your automodel object to specify files to use:

a = automodel(...) a.toplib = '${LIB}/top_allh.lib' a.parlib = 'my_parameters.lib' a.make()

Ben Webb, Modeller Caretaker