[Chimera-users] zone command

Francesco Pietra chiendarret at gmail.com
Wed Nov 12 08:43:04 PST 2008

A polypeptide was docked onto a protein that already carried ligands.
Then, molecular dynamics of the complex was carried out. To do this, a
single PDB file was created with the program ptraj of Amber.

Although ptraj removes chain labels, TER lines, etc., renumbering all
the residues in a single sequence, I know, from the ligand positions,
the corresponding numbering for the chains and for the polypeptide.

Which is the best procedure to map around certain groups of amino
acids of the protein, i.e., those that constitute the
experimentally-evaluated binding site? I want to take notice of which
residues of the polypeptide are most involved in the binding.


francesco pietra

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