The only possible way to view representation of the configuration volume of the ligand was the representation of all frames of the ligand along the trajectory. By the way its not quite understand for me in one case the measurement of the diffusion coefficient could be better than MSD which is the measure of the random displacement of the particle itself. ( my current taks is the examination of the ligand mobility as the rigid-body within ligand-binding-cavity).
Also I wounder to know about some possible way to measure dynamics of the non-covalent bonding along the trajectories. E.g I've defined in index file all polar and aromatic residues of the ligand-binding pocket. IS there any way to calculate all possible bonds (I want to measure the lifetime of that bonds as well as its occurrence in case of different ligands) between ligand and that side-chains along the trajectory ? James 2013/4/23 Justin Lemkul <jalem...@vt.edu> > > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
