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

James Starlight jmsstarlight at gmail.com
Wed Apr 24 09:26:26 CEST 2013

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

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 ?


2013/4/23 Justin Lemkul <jalemkul at 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
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