# What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?

I need to lightly verify a set of docking simulations from the reference RMSD of the outputs, and as we all know reference RMSD depends on the initial coordinates of the ligand set. What value of reference RMSD after docking from any starting coordinate would be considered outrageous to have?

• Based on your terminology I am guessing you are using Autodock Vina. Right? Oct 8 '19 at 13:10
• @MatteoFerla Any docking software actually, but do u have an idea for Autodock Vina? I am trying to find a general RMSD pose range for results in docking simulation Oct 10 '19 at 4:17
• I think I follow your question now, sorry. It utterly depends how much you know of where the ligand actually goes. I don't like VINA and use Rosetta would use the score command with the reference structure given with the -in:file:native flag, while all the other poses as -s * as normal. But in a Rosetta docking_protocol run how much a ligand wonders off course depends on the flag you set, hence my confusion. Oct 10 '19 at 6:49

Let's get some definitions out of the way:

RMSD, root mean square deviation, is a metric of distance of molecule A and molecule B. Think of it as average euclidean distance. It us casually called just 'deviation', but has nothing to do with standard deviation (the root of variance, 2nd moment). The units are Ångström.