On 12/12/16 5:09 PM, Mahesh Velusamy wrote: > 1.what is the difference between these two restraints in terms (when to > use) usage ?
Soft sphere penalizes interpenetration of two atoms's vdw spheres using a simple harmonic function. Lennard Jones uses the full 6-12 potential. Soft sphere is cheaper since you can use a shorter nonbond cutoff distance, but less accurate because you miss the long range attractive component. You can use whichever one you want - it doesn't make a huge amount of difference.
> 3.Why dynamic_sphere kept as False in this script > https://salilab.org/modeller/wiki/Mutate%20model ?
Because in that script LJ interactions are used instead. You can certainly use dynamic_sphere instead of dynamic_lennard if you like.
Ben Webb, Modeller Caretaker