Vina flexible docking about autodock-vina HOT 4 OPEN

The second picture looks like protein sidechains, but the first one does not. I don't think one is the output of the other.

from autodock-vina.

Hi @aditya-jugade Just in case you didn't notice this, there will be two types of output files after splitting the flexible docking output. For example, splitting the flexible docking output file in the example which contains 8 models, will produce 16 files, 8 for ligand and 8 for the flexible sidechains. They are named differently:

./vina_split 1fpu_ligand_flex_vina_out.pdbqt
gives you
eight 1fpu_ligand_flex_vina_out_ligand_<mode number>.pdbqt
and
another eight 1fpu_ligand_flex_vina_out_flex_<mode number>.pdbqt

What you showed in the picture looks like the latter type of the files, which contains only the flexible sidechains. They look broken because backbone atoms are not changing in the docking, and thus they are not reported as part of the docking outputs.

from autodock-vina.

from autodock-vina.

There is no ligand in the second picture.

from autodock-vina.