On 6/15/17 4:13 AM, bcuevas wrote: > 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: https://salilab.org/modeller/9.18/manual/node227.html

Ben Webb, Modeller Caretaker