[gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD

[Quin K]

Hi

I noted when I used Autodock vina for docking and used the converted back
.mol2 file from .pdbqt format, there were a lot of changes in the molecule
than the molecule I initially submitted to Vina for docking. Like the *atomic
charges were different. *
Is this normal? or is there a way to use the original DFT optimized
molecule with current docking orientation of Vina output file??
Also noted that there were missing atoms like hydrogens.
Last time I tried this simulation the ligand got detached from binding site
after like 20 ns. This could probably be a main reason for that because I
never refined the molecule to adjust for changed charges etc.

Kindly give your opinion
Thanks!
Regards!