Re: [AMBER] Ligand RMSD

From: David A Case <>
Date: Mon, 18 Jul 2016 15:49:48 -0400

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.


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Received on Mon Jul 18 2016 - 13:00:03 PDT
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