[AMBER] Percent occupancy of a hydrogen bond

From: menwer momo <masalmeh2007.yahoo.com>
Date: Thu, 7 Aug 2014 05:00:46 -0700


In a protein-DNA complex, a certain hydrogen bond between two amino acids has 3.4 angstrom distance between acceptor and donor atoms.
Hydrogen bond analysis shows that the occupancy of this bond during production runs is 30%, does this reflect that the bond is not stable?
Or  is it possible that the reason of this low percent occupancy is conformational change in the side chains of the two amino acids through production runs, and does not necessarily mean that this bond is not stable in reality?

note : I used ambpdb to create a pdb file after the production runs, it showed that their is a change in the conformation of the side chains, the distance between the acceptor and donor became 4 angstrom.

Thank you.
AMBER mailing list
Received on Thu Aug 07 2014 - 05:30:03 PDT
Custom Search