ADL: (no subject)

Ruth Huey rhuey at
Tue Mar 11 08:24:27 PDT 2008

jsmith48 at wrote:
> Hello, I'm trying to convert a PDB receptor file to a PDBQT file  for docking and I get the following error:
>     Cannot create the PDBQT file, all atoms do not have an autodock_element field
> Has anyone ever encountered this issue? If not how are you able to take a pdb file and prepare it for docking?  Thank you!
> ________________________________________________
> --- ADL: AutoDock List  --- ---

In ADT, this error message occurs when one or more atoms in a file does 
not have an 'autodock_element' attribute.  It is not possible to write a 
'pdbqt' file if all the atoms do not have the 't' property which is 
referenced as 'autodock_element' in ADT.

In ADT, you can use 'Edit->Atoms->Assign AD4 type' to assign this 
property to the all the atoms in your receptor.
[fyi: it acts on all the atoms in the 'current selection' which by 
default expands to all molecules when nothing is selected.]


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