ADL: Set Number of Torsions with scripts

Dinler Antunes dinler at gmail.com
Fri Mar 11 12:10:07 PST 2016


Dear fellow subscribers,

I am running some experiments with peptide ligands and I want to run
several dockings with ligands with different sizes, but always sampling a
small subset of the total amount of (possible) flexible bonds. The optional
feature "Set Number of Torsions" available in ADT would be perfect for this
task. I just want to provide the ligand and the number of bonds to be
flexible (let's say 6), and get a pdbqt file with TORSDOF 6. At this point
doesn't matter to me which bonds are being sampled. However, I want to do
this in an automated way (script) and prepare_ligand4.py doesn't seem to
allow to "set the number" of active torsions (without providing a specific
list of atoms with -I). There is any way of automatically generating a
pdbqt file with a fixed number of active torsions, regardless of the total
number of bonds in the input pdb?


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