Thanks for the informative explanation Prof. Case
On Mon, Jul 18, 2016 at 8:49 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Jul 18, 2016, anu chandra wrote:
> >
> > After a 50 ns long simulation, I am trying to analyse the change in
> ligand
> > structure and binding pose from it initial docked pose in a
> protein-ligand
> > complex. For this, I am trying to calculate the ligand rmsd from its
> > initial docked pose using following different cpptraj commands,
> >
> > 1. here I first align the protein-ligand complex and then do a no-fit
> rmsd
> > for ligand,
>
> This sounds like what you want, at least to me. However, think carefully
> about whether you want to align the entire 450 residue protein or not. It
> might be more informative to align the protein residues in the vicinity of
> the binding site. Or to align just the secondary structure elements of the
> protein. etc.
>
> Try different alignment schemes, visualize the resulting trajectories, and
> see
> which ones seem most informative. There is no "right answer", and no
> single
> number that will suffice.
>
> > 2. My second try was to do a straight-forward rmsd calculation for ligand
> > alone, without any prior aligning of protein-ligand complex ( presuming
> > that ligand align itself)
>
> This tells you the change in the ligand conformation itself, with no
> reference
> to whether its pose with repect to the protein has changed or not. This
> might
> be a useful thing to know, but it is not what you asked in the first
> sentence
> of your post.
>
> ....dac
>
>
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Received on Tue Jul 19 2016 - 08:00:03 PDT
