[gmx-users] Re: protein-ligand interactions in charmm force field

Justin Lemkul jalemkul at vt.edu
Tue Apr 23 19:14:36 CEST 2013

On 4/23/13 10:18 AM, James Starlight wrote:
> Justin,
> as the example I have 2 systems consisted of receptor completed with 2
> different ligands.
> After 100ns of production run I've realized that both of that ligands has
> the same degree of conformational dynamics on internal degrees of freedom (
> the same RMSD as the measure of internal mobility of that compounds). But
> the main difference was in the mobility of the smaller agonist molecule
> (movement inside the ligand-binding pocket   in comparison to the bulkier
> antagonist. So as consequence I've obtained  higher value of the MSD in
> case of smaller ligand. Could the MSD be representative measure of such
> whole-body motion of the ligand ? What advantages have the calculation of
> the diffusion coefficient ( which could be calculated from MSD )?

Maybe.  What other studies have examined similar properties, and what did they 

> 2) How I could visualize such ligand mobility ? For example for dynamics on
> internal degrees of freedom Principal components analysis could give best
> representation of conformational mobility.
> In case when I want to explore diffusional-behavior I should obtain
> representation of some confrontational volume (the surface within
> ligand-binding cavity  accessible for the ligand). What Gromac's tools
> could be useful for that?

Chapter 8 of the manual.  There may or may not be an existing Gromacs tool that 
will do the things you want.  The only way to find out is to go looking.



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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