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: