How to handle electric charges？

[guyuehuo]

Hello, I noticed that the charge value is crucial in RLdock energy calculation. I would like to ask about the impact of the accuracy of the charge value. When I only have the pdb file, is it reliable to use openbabel to calculate the charge？

[zhou0312]

Hi, the partial charge values are indeed crucial for RLDOCK energy calculation. However, we have not evaluated the impacts on the results with different partial charges methods.

In RLDOCK, the charge method used for ligand is AM1-BCC and the charge method used for standard nucleotides in RNA is AMBER ff14SB. You can use UCSF Chimera to protonate (i.e., add hydrogens) and add AM1-BCC partial charges to ligand. Chimera can also handle RNA.

As for openbabel, If it can generate AM1-BCC charges, it will also work.

[jj-dash]

Chimera 1.15 could not add charges to the terminal 5' phosphate. How to achieve that.