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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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How can I calculate RMSD in hydrated Vina? #238

Open ariadnallop opened 10 months ago

ariadnallop commented 10 months ago

I have just run a docking simulation using the hydrated Vina protocol (link to protocol) for the first time. In the next step, I want to calculate the RMSD between the results and the crystal ligands. The problem is that water molecules are bonded to the ligand, making them different molecules, and it seems impossible to calculate. Also, the last step I took was executing dry.py, and sometimes, when I execute dry.py, I encounter an IndexError.

IndexError: index 41 is out of bounds for axis 2 with size 41

rwxayheee commented 9 months ago

Hi @ariadnallop, I have a possible but maybe not the best solution - The prepared ligand pdbqt file should have the indices that can possibly be used to map with the canonical Smiles. Using the Smiles & indices, you could register the docking pose as a rdkit molecule/conformer. If you are able to read the reference structure + docked pose as rdkit molecules, please consider the following package for RMSD calculation: https://github.com/rdkit/rdkit/tree/master/Contrib/CalcLigRMSD