VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Aug 12 2008 - 10:05:46 CDT

Dear all,
i am making a movie in vmd and want to display only those hydrogen
bonds which are formed between a protein and water molecules
(protein-protein HB are ok as well).
is there any way to do it?

the problem is if i display only protein (no water) and choose Hbonds
representation, then only protein-protein HB are displayed.
if i display everything (protein+water), then protein-water HBs are
visually hidden by numerous useless hydrogen bonds between water
molecules. 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati