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).

On 31 Oct 2016, at 16:44, Modeller Caretaker <modeller-care@salilab.org> wrote:

On 10/31/16 7:23 AM, David De Sancho wrote:
However, I found out that for using
energy more tricky bits seem to be required, starting by an alignment
between two sequences.

Just use the complete_pdb script, which assigns CHARMM atom types so that the energy can be calculated. See
https://salilab.org/modeller/9.17/manual/node455.html

Ben Webb, Modeller Caretaker
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