Thanks very much! Am trying what you suggest today. :)
On 11 May 2011 19:38, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > I was hoping someone might be able to set me in the right direction as to
> a
> > query I had regarding amber 10.
> >
> > I've run a long MD simulation with explicit waters of a ligand bound to a
> > protein. I would like to identify which protein residues make contact
> with
> > the ligand, so that I know what residues to look at in a per-residue
> > decomposition.
> >
> > I've been playing with the contacts command in ptraj. In the results, I
> get
> > two columns: example:
>
> The contacts only tells you the number of contacts, not what they are...
> For this, I would use the hbond command in ptraj instead.
>
> Alternatively, I would cluster the trajectory, visualize the
> resulting average structures and then only show residues "near" the ligand
> and identify by eye.
>
> --tec3
>
>
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Received on Fri May 13 2011 - 04:30:02 PDT
