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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
