[gmx-users] Fwd:

Justin Lemkul jalemkul at vt.edu
Tue Aug 15 14:02:57 CEST 2017

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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