ADL: autodock Digest, Vol 182, Issue 12

Diogo Martins diogo.stmart at
Wed Apr 15 10:46:35 PDT 2020


Please note that HDC, OAA, OAC OAHD and OACC are not standard atom types.
Unless you created these atom types, there's something wrong.

I recommend GNU parallel. If you have a text file with all the docking
commands, one command in each line:

$ cat commands.list
autodock4 -p dock1.dpf -l dock1.dlg
autodock4 -p dock2.dpf -l dock2.dlg
autodock4 -p dockN.dpf -l dockN.dlg

GNU parallel can execute these single-threaded processes in parallel:
$ parallel -j 8 < commands.list

Best regards,

On Wed, 15 Apr 2020 at 04:00, venkat <azbvenkat at> wrote:

> Hello,
> Thank you very much Martins  and Hubertus ,  Now I am able to perform the
> autogrid and autodock. As per your guidance, I rerun the script
> prepare_dpf  with option -p ligand_types, for that I used following
> command.
>  *pythonsh  ../Utilities24/ -d TRI_PLPRO_COM_LIN/ -r
> plpro.pdbqt -p npts="40,40,40" -p gridcenter="-19.198,53.911,-34.169" -p
> ligand_types="C Cl HD HDC OA OAA OAC OAHD OACC NA SA" -o grid.gpf*
> After grid generation I modified affinity map according to the
> ligand_types.
> I doubt/clarification, How to perform Autodock in HPC clusters (let say
> utilize all processor which available in machine), because, through script
> I submitted the job it only tacking one processor out of 8. Following
> script I used to submit job
> #!/bin/csh
> cd /Dockings
> ls  >2docking.list
> foreach d (`cat 8docking.list`)
> echo $d
> cd $d
> autodock4 -p $d.dpf -l $d.dlg
> cp $d.dlg ../../dlgs/
> cd ..
> end
> kindly  provide your valuable answer
> Thank you
> Sincerely
> venkatesh
> ________________________________________________
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