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
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