Wrong RMSD calculation?

[lkfo415579]

I noticed there is a problem with the docking pose generation script you provided #Docking_CASF2016_CoreSet.ipynb.

In dock_compound function, there is a line
result['rmsd'] = Chem.rdMolAlign.AlignMol(opt_mol, real_mol, atomMap=list(zip(opt.noHidx,opt.noHidx))).

This means you are aligning opt_mol to real_mol, then calculate the rmsd, when I delete this line, the docking pose will become much worse than before. This operation is only used in the molecule generation task but not in the docking task, it will neglect the error of rotation and translation of ligand.
You should output the conformer to a file and then use obrms(from openbabel) to calculate the real reliable rmsd.

I reproduced your experiment, using the code directly from your code the result successful rate is correct and is about 62%.
After I removed the alignment line and redo the experiments, the successful rate drops down to 41%. (percentage of docking pose is <2A RMSD compare to crystal-structure)

[Glinttsd]

Hi, as for it will neglect the error of rotation and translation of ligand, I have a question. Doesn't aligning mean neglecting the relative postion error instead of rotation and translation?

[lkfo415579]

Hi, as for it will neglect the error of rotation and translation of ligand, I have a question. Doesn't aligning mean neglecting the relative postion error instead of rotation and translation?

I think they are the same meaning.