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

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 13:03:50 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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