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...@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
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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