Re: [modeller_usage] energy of interface between selections

[David De Sancho <>]

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

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 <" class="">> 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
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