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

Justin Lemkul jalemkul at vt.edu
Wed Apr 24 14:22:22 CEST 2013

On 4/24/13 3:26 AM, James Starlight wrote:
> 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 ?

What you're describing are nonbonded interactions, not bonds.  There are a 
variety of quantities you can measure, like hydrogen bonds, contacts, etc.  You 
can post-process to get various autocorrelations and lifetimes.  Again, Chapter 
8 is your friend here.



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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