[gmx-users] distance between protein and ligand

Justin Lemkul jalemkul at vt.edu
Tue Oct 9 15:00:02 CEST 2012

On 10/9/12 12:48 AM, Archana Sonawani wrote:
> Hi,
> I have simulated a protein-ligand complex for 5ns. I checked distance
> between the important residues of protein and the ligand using g_dist. My
> question is can the distance between the two groups decrease  from the
> initial distance (docked complex as starting structure for simulation). I
> know it may increase or may remain same at the end of the simulation.
> for example: starting distance is 0.77nm and final distance is 0.8nm but
> the intermediate course of simulation (around 3ns) it has decreased upto
> 0.65. The complex shows stability after 2ns. While the SASA between the two
> groups is around 6.3 nm2  throughout the simulation which is very high.
> This is very contradicting result. Is something wrong in the simulation?

I don't see anything wrong at all, though I don't understand how the SASA 
calculation connects with any of this.  That's an awfully large value for 
interfacial SASA, unless the ligand is rather large.

Distances can increase or decrease depending on the nature of the interactions 
and small conformational changes in either the ligand or the protein.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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