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

James Starlight jmsstarlight at gmail.com
Tue Apr 23 16:18:18 CEST 2013


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 )?

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?


2013/2/7 Justin Lemkul <jalemkul at vt.edu>

> On 2/7/13 5:15 AM, James Starlight wrote:
>> Justin,
>> Thanks again for suggestion. I've found that g_mindist is exactly what
>> I need. I'm not quite sure how I could use that tools to find all
>> possible interactions between my ligand and several polar residues
>> defined in the ndx file ( I have no problem only when I examined
>> manually each possible interaction separately). Finally I'm not quite
> There's no way to do automated screening for these types of things.
>  You'll have to choose groups of interest and make corresponding index
> groups for analysis.
>  sure about number of contacts calculated by g_mindist. E.g I've
>> examined it for my ligand ( having 3 polar atoms and large hydrophobic
>> ring)  and 1 serine residue ( 1 polar side chain group ). As the
>> ouitput I've obtain 60 maximum contact number (and 10- minimum). Why
>> maximum number was so big ?
> Sounds about right if you're using the whole serine residue, or even just
> its side chain.  The number of contacts (if memory serves, but do check the
> code!) is at most N^2, where N is the total number of atoms in both of the
> chosen groups.
>  Some another question- I want to find a way to esstimate average
>> mobility of my ligands in the ligand binding pocket.
>> For example I have 2 different complexes of my protein with 2
>> different ligands- one of that liugand is big and occupy big spacy
>> whithin protein interiour ( so that ligand is less mobile). On the
>> contrary the second ligand is samller and flexible so it muast be more
>> mobile within protein and it seen visually during visualisation of the
>> md trajectory. But how it could be estimated in some values ?
> You can define mobility in a lot of ways - RMSF, diffusion constant, RMSD,
> etc.
> -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>
> ==============================**==========
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