[phenixbb] wander wall interaction

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Wed Dec 1 08:58:02 PST 2010

Hi Subhash,

> 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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