Dear Ben Thanks for the quick response. However I find something really puzzling for a few tests. Mainly, that interface energy turns out to be unfavourable. In the link below I include a gist with a self explanatory example of how this turns out to be. It corresponds to the interface between two helices in the designed a3D protein but I’ve tried with others too. https://gist.github.com/daviddesancho/c854203311ec431d0c17fcfff5055e8c https://gist.github.com/daviddesancho/c854203311ec431d0c17fcfff5055e8c Surely there is something about my selections that’s not right, but any hints at what’s going on would be very helpful. Thanks,
David
> On 26 Oct 2016, at 22:00, Modeller Caretaker modeller-care@salilab.org wrote: > > On 10/26/2016 08:41 AM, David De Sancho wrote: >> I’m handling a problem where it is important to evaluate energies of >> interfacial residues (e.g. interface residues between two helices in a >> protein). In order to carry out this energy evaluation with Modeller, I >> start by producing a model for the protein. Then I generate two >> selections (e.g. one for each helix). Would it be possible to calculate >> the energy for residues in the interface between both selections? > > Calculating the energy of only the interactions between selections s1 and s2 isn't possible to do directly in Modeller, but there's a simple workaround: calculate the energy of the union s1+s2, then subtract the two energies of s1 and s2 by themselves. You'll probably also want to set nonbonded_sel_atoms to 2: > https://salilab.org/modeller/9.17/manual/node140.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage