[gmx-users] Fwd:

[Justin Lemkul]

On 8/15/17 1:52 AM, saranya wrote:
> Hi,
> I have done protein-drug simulations for 100ns. While calculating the hydrogen
> bond between the protein-drug complex I am getting only 2 hydrogen bonds.
> The number of H-bond formation is very low I have a question about is there
> any influence of the drug in my protein?
To answer that, you need to do simulations of the apo protein and 
compare whatever relevant structural metrics there are (not H-bonds, as 
these tell you about the ligand-protein interactions but nothing about 
the impact on the protein structure).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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