[phenixbb] wander wall interaction
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Wed Dec 1 08:58:02 PST 2010
> I am working on a enzyme-ligand complex structure. For some analysis I need to
> remove wander wall interactions between protein and ligand. How can I do that
> Phenix? Something similar to igroup statement in CNS?
A simple trick is to assign altloc characters to the ligand and the parts of the
protein that shouldn't interact, e.g. set column 17 of the protein atom records
to "A" and in all ligand records assign "B". There will be no van-der-Waals
interactions between A and B, only between blank-X and X-X, where X is A or B.
The situations where you'd use an igroup statement in CNS are handled more
automatically in phenix, via inspection of altlocs and occupancies. I'm curious
why you'd want to turn off the van-der-Waals interactions too the ligand.
Without them it could bump into the protein, which isn't physically possible.
Could you explain?
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