[gmx-users] Fwd:

Justin Lemkul jalemkul at vt.edu
Wed Aug 16 17:54:25 CEST 2017

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 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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