| Thanks again As you suggest, the complete_pdb script helps a lot in building the model from the PDB file. For the energy calculation I still have some issues. I guess that for calculating energies of interfaces we should care primarily for the LJ and Coulomb terms. So I have added a make_restraints() function so that for each selection we generate restraints for both terms. This gives LJ and Coulomb energies for selections. Although again I do not seem to recover sensible results (energies for s0s1, s0 and s1 are comparable). Does this make sense for the energy estimation of interfaces? David
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