Hi There,
I am trying to perform a protein-protein docking simmulation between two proteins, A and B. Both protein has bound ligand, I know Rosetta cannot run with both ligand, So in a run, I remove ligand. But, I would like to give constrain 5A residue of surrounding the ligand. I already checked the constrain tutorial but I found that atom pair only give CA of amino acid. Atom pair wouldn't work for me. My question is I want to give full amino acid as a constraint. Totally will be around 10 amino acid as a constraint in each protein. Could you please help me with this? Please let me how can configuration and constraints file.
Thanks in advanced.
Haresh
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Post Situation:
I'm not quite sure how you're envisioning the constraints.
Typically in Rosetta, how we set up constraints is that we have some geometry (e.g. an atom-atom distance, an angle, a torsion, a distance from an XYZ coordinate, etc.) which can be rendered into some number. We then look to see how much that number deviates from a desired value, and convert that geometry measurement into a score bonus/penalty based on a given functional mapping. -- There are more advanced constraints, but they're elaborations on the general concept of measuring some geometric feature and then mapping that measurement onto a score.
So when you say you want to give a full amino acid as a constraint, what do you mean by that? What geometry does that involve? How would you measure a deviation from an "ideal" geometry?
By the way, while atom pair constraints are typically used with Calpha-Calpha distances, they can be set up between any pair of atoms in the protein. Not just Calphas, and not just protein residues, either. So long as the two atoms are present, you can restrain them with the AtomPair constraint.