I am currently modelling a protein, I have so far generated 160 models of this protein.
I then remve models that have backbone clashes via energy minimisation. Models with a -ve energy after minimisation were considered to have no clashes where as proteins that have +ve energy after minimisation were considered to have a clash.
I then looked at structures that had -ve energy and some of them had severe backbone clashes, where as other model with a +ve energy did not.
Is there any reason for this? Which is the best way (rather than eye) to determine if a protein has a clash?
I performed minimisation in Chimera. I did 100 steps, with 0.02 angstrom movement and no fixed atoms.
Also, is it better to look at the energy or the gradient norm? I used energy because I do not know what the gradient norm is.