Hi,
I have 22 mer DNA and after the completion of production, I wanted to
calculate the Hoogstein H-bonding distance. but surprisingly I fail to get
the data for res 22 (dG22). Why is it so? Is there any problem in the
script?
The script that I'm using is as follows :
trajin X.mdcrd
#-- Donors for Hoogstein h-bond
donor mask :DG.O6
donor mask :DG.N7
#-- Acceptors for Hoogstein h-bond
acceptor mask :DG.N1 :DG.H1
acceptor mask :DG.N2 :DG.H21
acceptor mask :DG.N2 :DG.H22
hbond distance 3.5 angle 120 solventneighbor 6 solventdonar WAT O
solventacceptor WAT OH1 solventacceptor WAT O H2
#-- series hbt is just a placeholder to ensure we get the full analysis. If
you don't
#have the word series you don't get a full analysis.
hbond print .05 series hbt
Thanks in advance..
Asfa.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 05 2010 - 23:30:03 PDT
