[Dock-fans] RMSD

[Scott Brozell]

Hi,

On Wed, 31 Oct 2007, Imtiaz M. wrote:

> In my dock.in file i have selected the RMSD as yes. now in my
> dock_ranked.mol2 I am getting a value RMSD 0.98786
> 
> Can any body tell me what that RMSD actually mean? i.e This root mean
> square deviation is between what and what?

Heavy atom RMSD between the final molecule pose and its initial structure.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileInput

Scott