[modeller_usage] Re: what is non-bonded restraints in modeller molpdf

On 2/15/25 11:43 AM, Li Xue via modeller_usage wrote: > I am trying to understand the components of modeller molpdf. Does anyone > know what the non-bonded restraints are, since modeller by default does > not calculate L-J nor electrostatics?

Modeller uses a soft-sphere potential for its nonbonded term. This is a simple harmonic potential applied when the interatomic distance is below the sum of the two radii. See https://salilab.org/modeller/10.6/manual/node131.html Since there is no long-range attractive component to this potential, one can use a relatively short cutoff distance: https://salilab.org/modeller/10.6/manual/node128.html

Ben Webb, Modeller Caretaker