Hi Enrico,
you may look at this script
https://github.com/DrrDom/rdkit-scripts/blob/master/rmsd_rdkit.py
It takes PDBQT as input and reference files and calc rmsd for the
largest common fragment if structures do not match each other. If there
are multiple models in the input file it will calc rmsd for all of them.
Do not forget supply SMILES files complementary to PDBQT, because PDB
does not contain bond orders. There is a built-in help message in the
script, but if you will have question regarding it you may ask me.
At least you may use it as a source to create your own script
suitable for your needs.
Kind regards,
Pavel.
On 30/03/2022 18:16, Enrico Martinez wrote:
Dear RDKIT users!
I am dealing with the analysis of the results of the docking poses
calculated via VINA and saved into the multi-model pdb. I need to find
a possibility to compare each docking pose with the pose in the X-ray
structure (which has similar but not
the identical ligand!) in order to find automatically the model (=
docking solution) with the positions of the
ligand similar to the X-ray structure?
Assuming that the both pdbs (docking poses, and X-ray structure) have
been superimposed (based on the protein atoms) how could I
automatically find the model (in the ensemble of 100 docking
solutions) where the ligand may resemble the X-ray pose (e.g. taking a
part of the ligand shared between the both structures as the reference
for comparison) ?
I would be grateful for any suggestions
With kind regards,
Enrico
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