ADL: change the string of rotatable bonds to inactive

Nehru V Sankaranarayanan nvsankaranar at vcu.edu
Mon Feb 24 13:01:14 PST 2014


Dear AutoDock users,

I have a huge library of molecules which needs to be docked to a receptor.
I have the molecules in .mol2 format. So I use the 'prepare_ligand4.py'
script from utilities to convert them to ".pdbqt" format.
So while doing this i wanted to inactivate few rotatable torsions.
I used the script as shown below.

./prepare_ligand4.py -l out.mol2 -o out.pdbqt -I '6_7_7_8'

After running this I expected  the bond between atom numbers 6 and 7; 7 and
8 to be inactive.
But I get an error saying
"ERROR: atoms at indices  7  and  8  have no common bond"
 when i check my .pdbqt file it shows to be active.

Whereas when i use ADT to load the ligand and select the torsion for
inactive, it does it right and i could see the .pdbqt file to have right
number of inactive torsions.
Any suggestions on fixing this torsion through command line would be of
great help.  The atom numbers for the fixed torsion for my entire library
is the same throughout. So i would like to do it in command line.
thanks,
Viji


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