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

[Scott Brozell]

Hi,

On Wed, 22 Oct 2008, amit dong wrote:

> So the amber score corresponds to which conformation?

Both ligand conformations because Amber score is an approximate
binding energy:
E(Complex) - [ E(Receptor) + E(Ligand) ]
See the top of this section:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore

But the ligand conformation in
protein.ligand.1.final_pose.amber.pdb
is the docked ligand; maybe that is what you seek ?

Scott

> On Tue, Oct 21, 2008 at 12:36 PM, Scott Brozell <sbrozell at scripps.edu>wrote:
> 
> > 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.