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

[amit dong]

Hi,

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.
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?
Any comments will be much appreciated.

Thanks
AD
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