I am using RosettaLigand application to dock a small molecule into the active site of an apo-protein structure of my interest. Instead of using a pre-generated conformers, I am using the "dummy" method of specifying proton_chi sampling for all freely rotating bonds. (So even for C-C or C-O bonds, I would add another proton_chi line below to add sampling for those chi angles)
My question is simple, but it seems pretty hard to google anywhere to find documentation for the parameters following PROTON_CHI
Sample PROTON_CHI line below:
PROTON_CHI 1 SAMPLES 2 0 180 EXTRA 1 20
Following SAMPLES, an sp2 proton would get "0 180" as two possible angles, and an sp3 proton would get "-60 60 180." Does anyone know what the two numbers following "EXTRA" mean? I've seen cases where it's just 0 (instead of 1 20), which I'm guessing means no sampling?
Essentially, I want to increase the number of sampling by manipulating these parameters, but I have no way of checking.
Any help will be appreciated.