ADL: WAT unrecognized

Pierre-Yves Dupont dodup64 at
Sun May 4 07:32:12 PDT 2008


In your selection command line, you are searching for residues called HOH
and in your pdb file, your residues are called WAT. The write command line
to select the water atoms in your case is :
Residue WAT* Atom*

HOH is not a keyword in autodock, it's just the name of the residue in your


Pierre-Yves Dupont

2008/5/4 Francesco Pietra <chiendarret at>:

> I am trying (1st time) to follow "Using autodock 4 with autodocktools: a
> tutorial", however directly with a protein model of mine, already arranged
> OK for Chimera.
> I was stuck in ADT immediately at the stage of selecting (Residue HOH*
> Atom *), getting warning
> "No new selection ::HOH*:*
> Accepting OK, no water selected (0 Molecules(s) in a red background in the
> center of the message-bar at bottom).
> Actually, the pdb loaded contains one molecule of water of crystallization
> (that I had deliberately left in for docking already carried out with other
> programs). The residue is called WAT, three line for O and the two H). Does
> autodock4 use a different name for water residue? I searched along manuals
> and archives; unable to find how non-standard residues are called in
> autodock4).
> Thanks
> francesco pietra
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