ADL: autodock Digest, Vol 182, Issue 12

venkat azbvenkat at gmail.com
Wed Apr 15 03:58:25 PDT 2020


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/prepare_gpf4.py -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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