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

[Justin Lemkul]

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 
measure?

> 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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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