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. https://gist.github.com/daviddesancho/125b446d79b75b8d346f564e967ebaa1 https://gist.github.com/daviddesancho/125b446d79b75b8d346f564e967ebaa1 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
> 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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage