unexpected very negative affinity score about uni-dock HOT 2 CLOSED

I know what happened. Unidock could not recognize atom G which allow Vina to sample the conformer of the macrocycle. If the input pdbqt file includes the atom of G, Unidock will give a unexpected result. The solution is to keep the macrocycle rigid.

from uni-dock.

Hi Dr. Xiao,
Thank you for reporting. We have noticed this situation and in Uni-Dock, the code actually takes the most negative affinity as baseline to calculate intramolecular score, whereas Vina 1.2.5 takes the first pose as baseline and sometimes very positive score can take place. Maybe it's a tradeoff and we choose to have very negative, instead of very positive. Indeed, they might both be cause by incorrect ligand input. In this case, MODEL 1 has clashes.

The code are as follows:

    poses.sort();
    // probably for bug very negative score
    m_model_gpu[l].set(poses[0].c);

Compared to ccsb-scripps/AutoDock-Vina@61df1f5
If you want us to reproduce this case, please provide us the receptor.

from uni-dock.