RMSD calculate

[Oscar Arrúa]

Good Afternoon,

I have a question. I try to compare the perfomance of the docking power between ODDT and Original Autodock Vina. I need to generate the pdbqt result file with ODDT for running the RMSD algorithm. Can I get that file with ODDT?

Autodock Vina Command:

vina --receptor 1a1e_protein.pdbqt --ligand 1a1e_ligand.pdbqt --config config.txt --out result_docking.pdbqt --energy_range 0 --log logs.txt  --num_modes 1

ODDT command:

oddt_cli 1a1e_ligand.mol2 --dock autodock_vina --receptor 1a1e_protein.pdb --size '(42.85146416401661,33.44809286043077,40.70584013381863)' --center '(41.4015,5.040000000000001,41.325)' --exhaustiveness 8  -O 1a1e_result.sdf

I attached the RMSD algorithm.

Thanks!

Oscar

[Maciek Wójcikowski]

Hi Oscar,

Running oddt_cli will ultimately run autodock_vina, so this is a bit redundant. If you want to run any comparison of vina results you have to set the seed with `--seed` parameter.

Calculating of RMSD is a more complex task, since with docking you would like to take symmetry into account. ODDT has `rmsd` function that has few options you can use, see https://oddt.readthedocs.io/en/latest/rst/oddt.html#oddt.spatial.rmsd

One tip for the future: when you end up writing manual parsers for molecular files. usually there might be a better way of doing such tasks.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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