ADL: map

Ruth Huey rhuey at
Thu Jan 31 09:26:39 PST 2008

Hi Floren,

Probably you have run into this problem because the atom type SA was 
missing from the ligand_types entry in the grid parameter file you used 
for the autogrid4 calculation and/or from the  ligand_types entry in the 
docking parameter file you used for the autodock4 calculation.
Unfortunately, there is currently a bug in ADT which affects the setup 
of input files for dockings involving flexible sidechains in the 
receptor. Specifically:
    If there are some atom types in ligand which are not also in the 
atom types of the flexible sidechains and if the ligand is specified 
(Docking->Ligand->) before the flexible residues file 
(Docking->Macromolecule->), potentially these types may be missing from 
the dpf. 

I am currently working on this issue but have not yet discovered a 
robust solution....

Meanwhile, you should check the completeness of the 'ligand_types' and 
'maps'  in the input dpf files.


Florenci V. Gonzalez wrote:
> Hello all,
> 	when I launch the docking it stops because it cannot find 
> the  "" file.
> I do not know why it does not create that file if the SA is an atom type.
>   Can anyone help me on this?
> Thanks,
> Floren
> ________________________________________________
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