The molecular structure changes after gnina docking simulation.

[Blue1993]

Issue summary

Docking simulation was performed using vina and gnina, respectively.

Next, we calculated the RMSD of the template and simulation results using the TOOL provided by “The Yang Zhang Lab”.

In the case of VINA, RMSD was calculated for simulation results, whereas RMSD cannot be calculated for most of gnina's results.

According to the log, the RMSD cannot be calculated because the template structure (structure before docking) and the structure of the simulation result (after gnina docking) are different.

Even when we performed visualization using pymol, we confirmed that the structures were different.

Why do these structural changes occur? In the case of docking simulation, isn't it about finding the pose (coordinates) of the molecule?

Additionally, how can RSMD be calculated in this case?

Steps to reproduce

Your system configuration

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[dkoes]

Can you provide examples of the different structures? GNINA will process the molecule with OpenBabel. Does obrms from OpenBabel work for computing the RMSD?