[gmx-users] Re: protein-ligand interactions in charmm force field
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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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