The Molecular Graphics Laboratory Forum

How does Autodock calculate the RMSD between the ref ligand and the docked conformations?
I get a certain RMSD value but when I build the conformations and calculate the RMSD with a different program I get different values, and yes I'm sure I'm comparing the same structures...
I know that there are a few algorithems to calculate the RMSD and I was woundering what does Autodock use.
Thanks

IF the rmsnosym keyword is in the dpf, AutoDock calculates the RMSD as you would expect:
RMSD = the square root of the [(sum of the squared-distances between the two positions of each atom ) divided by the number of atoms].

IF rmsnosym keyword is not in the dpf, the RMSD is calculated as the square root of the sum of the squared-distances between each atom in one conformation and the closest atom (which has not already been used) of the same element in the other divided by the number of atoms.

(see 'sqhypotenuse(x,y,z) in constants.h; also look at getrms.h and getrms.cc)