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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users