If you want to see the vdw interaction is their or not run a per-residue
binding free energy with ligand and that particular residue/s of the vDw
term is zero then no interaction and if interaction is printing then there
is interaction.
On Wed, May 28, 2014 at 3:37 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, 2014-05-28 at 21:27 +0800, Nitin Sharma wrote:
> > Dear amber users,
> >
> > Is there any command to check non bonded interactions like vander
> > waal's interactions between ligand and selected residues?
>
> You can see if MMPBSA.py's decomposition options or the "pairwise"
> command in cpptraj will do what you want. These are all described in
> the Amber 14 manual.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed May 28 2014 - 07:00:04 PDT
