Hello,
I believe that one reason that one cannot compare molpdf scores between models of different proteins is that it depends on the number of atoms in the protein- more atoms means a higher molpdf, even if it is a "good" model. Does this mean that if one is trying to do an all hydrogen model that the molpdfs will be much higher than that for the same protein modeled without hydrogens?
The reason that I ask is that I am modeling a pentamer with an all hydrogen model, and each time the modeling stops after a few steps with the moldpdf stuck slightly higher than 100,000 (which is the default max_molpdf value) and then moves on to the next model, where this happens again (and again...). I assume that this is because of all of the additional hydrogens, and that if I just increase max_molpdf to 200,000 things should be fine.
Is my underlying assumption correct?
Thanks