That's straightforward - just subclass the allhmodel class rather than
automodel, i.e. replace the line
class mymodel(automodel):
with
class mymodel(allhmodel):
You should be aware that including hydrogens will result in your models
taking roughly 4 times as long to build (since you have roughly twice as
many atoms).
and a substrate that's on one
of the templates
Just add relevant BLK residues ("." characters) to your alignment, and
turn on env.io.hetatm. See the examples in the manual and tutorial.
And by the way,
modeller does not make simmulated annealing wrigth?
I'm not sure what you mean. If you mean, "does Modeller do simulated
annealing?" then yes, it does. The standard model building procedure
combines conjugate gradients minimization with molecular dynamics
simulated annealing refinement.