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

[Modeller Caretaker <>]

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
-- 
             https://salilab.org/modeller/
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