[gmx-users] Fwd:

[Justin Lemkul]

On 8/16/17 3:05 AM, saranya wrote:
> Dear Justin,
>
> Thank you for your kind response.
>
> I have made all the basic analysis and yes there are certain structural
> changes that i have expected. But my clarification is as follows.
> Initially, there were 6 H-bonds and when it reach around 15ns it is reduced
> to 1 or 2. Do the effect of ligand over protein increase/decrease with a
> number of hydrogen bonds? Or even a single bond between protein and ligand
> is more sufficient to bring necessary changes to a protein?

There are a lot of unknowns here.  Maybe 6 H-bonds is spurious - how did 
you generate that pose?  If it's from docking, it may not be real.  Even 
if it's from a crystal structure, it may not represent the most probable 
state in solution.  Maybe the ligand topology is inadequate - how did 
you generate and validate it?

-Justin

-- 
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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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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