I am using Modeller to include mutations in the interface of
protein-protein complexes. One of the crucial parts of my work here is
to characterize and improve the available methods including water at the
interface, and I wanted to use the restraints related with hydrogen bond
energy since I think they are very important in this.
Modeller doesn't include any restraints for hydrogen bonding, or model
water explicitly for that matter. The assumption is that the template
structure already contains this information, so the homology-derived
restraints will implicitly take care of this in the output model.
However, I can not
find in the documentation how to use the Physical.h_bonds as a
restraint, since I don't know how this energy function is defined and
what is its input.
The various physical.* types are just groups or bins into which you can
place restraints, for easier reporting - they're not restraints
themselves. I think the only place physical.h_bonds is used in Modeller
is for alpha-helix restraints: