ADL: autodock Digest, Vol 46, Issue 14

Vinay Kumar ksvinaykumar at
Tue Jan 22 09:46:50 PST 2008

Helo deepthi,

> I am using autodock4. I am having problems when i run autogrid. it says
> there is some problem with rigid file.
> could this be due to active site. I mean.. i dont exactly know the active site of my protein, so I chose some
> residue. could it be due to this??

It has nothing to do with this, select a suitable grid box size that
would encompass your protein and perform a blind docking. this would
give a insight into possible active site residues.

> the error message that I get is
> /compute/deepthi/AUTODOCK/i86Linux2/autogrid4
> /compute/deepthi/AUTODOCK/i86Linux2/autogrid4: ERROR:  can't find or open
> receptor PDBQT file "protein_rigid.pdbqt".
> /compute/deepthi/AUTODOCK/i86Linux2/autogrid4: ERROR:  Unsuccessful
> completion.
 This error would occur, if you are NOT selecting /or/ saving
correctly the protein (receptor) file name as "protein_rigid.pdbqt"

> why is this happening?
> please help!!
 Save correctly, and choose the saved protein_rigid.pdbqt file to run
your autogrid and autodock programs...
Hope this helps,


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