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

[Justin Lemkul]

On 12/30/19 10:05 AM, Quin K 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??

Consult the Vina documentation for how to control topology aspects like 
charges.

> Also noted that there were missing atoms like hydrogens.

This is also probably a Vina convention, to speed up the calculation. 
This would explain why charges changed. You can't just delete hydrogens 
without accounting for their partial charges.

> 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.

The topology you used for MD and the charges used in docking likely have 
no relationship to one another, and if the pose was really that heavily 
influenced by these factors, you probably would have observed a change 
in the binding pose even after energy minimization.

-Justin

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Justin A. Lemkul, Ph.D.
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