[Dock-fans] output files of amber-dock rescoring

[Scott Brozell]

Hi,

On Mon, 20 Oct 2008, amit dong wrote:

> I am carrying out Amber rescoring calculations on a couple of ligands using
> dock6.2.
> I get two output files for each ligand: ligand.1.final_pose.amber.pdb and
> protein.ligand.1.final_pose.amber.pdb.

Thus, you have specified amber_score_movable_region as ligand
since you did not get protein.final_pose.amber.pdb.
See the tail of this section
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore.

> But the coordinates of ligand in both the files are quite different. I
> believe the above two files correspond to final ligand conformation with and
> without protein. Then why are the coordinates different. What is going wrong
> here?

Yes, the coordinates should be different because moving the ligand alone
should be different than moving the ligand in the presence of an immovable
receptor.  This should all be clear via visualization of these files as well
as of the initial coordinates.

Scott