ADL: ./autodock cant open or find .dpf

Gonçalo Justino goncalo.justino at gmail.com
Tue Feb 12 07:37:13 PST 2008


if you haven't done so already, try to run autodock4 from the folder with
the actual files (ligand, receptor, maps and such), copying the files and
not using symbolic links.

It worked for me when I got the same message...

Gonçalo


On 12/02/2008, Miguel Quiliano Meza <qilime at yahoo.es> wrote:
>
> Hi dockers.
>
> I have a little question. I have been runnig ./autodock4 but in the
> terminal appears this:
>
>
> ../autodock4: WARNING: the atom type (N) of atom number 3 could not be
> found;
>         check that this atom type 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.
>
> ../autodock4: WARNING: the atom type (SA) of atom number 7 could not be
> found;
>         check that this atom type 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.
>
> ../autodock4: WARNING: the atom type (N) of atom number 15 could not be
> found;
>         check that this atom type 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.
>
> ../autodock4: WARNING: the atom type (N) of atom number 19 could not be
> found;
>         check that this atom type 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.
>
> So I changed my file .dpf according to the message. but Now appear this:
>
> ../autodock4: can't find or open parameter file .dpf
>
> ../autodock4: Unsuccessful Completion.
>
> By the way, autogrid4 produces N.map and SA.map so.. what is the problem?
>
> I would like very greateful if you help me.
>
> thanks in advance.
>
> Miguel.
>
>
>
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>
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>
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>



-- 
Gonçalo Justino
PostDoctoral Fellow @ REQUIMTE/CQFB www.requimte.pt

Chemical Chiseler&Annihilator
// Errare humanum est, perseverare diabolicum: you only die once.


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