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

[Justin Lemkul]

On 12/30/19 1:51 PM, Quin K wrote:
> Further to following email, is it OK to do an energy minimization with
> Gaussian16 so the molecule is refined before MD simulation with Gromacs?

What would be the purpose? A gas-phase optimized geometry has no 
relationship to the pose adopted by a molecule upon binding to its receptor.

> If such an energy minimization is done should I use DFT ?

Depends on the force field you're using. Most biomolecular force fields 
do not use DFT for most calculations. If this goes back to our original 
discussion about your CGenFF parameters, I beg you to follow the advice 
I already gave - read the CGenFF paper. It tells you the *exact* model 
chemistries you should use for everything to ensure compatibility with 
the CHARMM force field.

> Would that affect the orientation at which molecule was docked with
> protein?

No, because the docking software changes the configuration.

-Justin

>
> 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!
>>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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