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

[Quin K]

Further to following email, is it OK to do an energy minimization with
Gaussian16 so the molecule is refined before MD simulation with Gromacs?
If such an energy minimization is done should I use DFT ?
Would that affect the orientation at which molecule was docked with
protein?

On Mon, Dec 30, 2019 at 8:35 PM Quin K <profiles.ke at gmail.com> wrote:

> 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!
>