> 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 Wed May 11 2011 - 12:00:05 PDT
