ADL: (no subject)

mmooney05 at qub.ac.uk mmooney05 at qub.ac.uk
Wed Feb 27 03:40:36 PST 2008


Hi all,
      I have the newest version of AutoDock installed (Autodock4.0.1) on my 
ubuntu 7.10 PC. There are a few things in regards to the autodock4 tutorial 
that I would like to question. Firstly, when I try to launch either an 
AutoGrid or AutoDock job from the GUI Launch button, it doesn't work. I can 
only use the command line to launch these jobs. Any suggestions as to why 
this is happening? Also, after following the tutorial and successfully 
generating all required files for a docking, I launch the job from the 
command line. I get the following error:

WARNING: the atom type (OA) of atom number 5 could not be found; check that 
this atom is listed after the "ligand_types" keyword in the DPF, and make 
sure to add a "map" keyword to the DPF for this atom type. Note that 
autodock will use the default atom type =1 instead.

The atom is not listed in the DPF after "atom types in ligand". This occurs 
for around 25 atoms in my docking. It also means that there are no grid 
maps generated for the atom types that are not specified.

I would appreciate any suggestions as to why this occurs, simply by 
following the tutorial.

Many Thanx,
           Maura


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