Hello there,
I have a traj of double beta-sheet (2strands on each sheet) stacking together via cross-sheet Q-Q sidechain H-bonding and hydrophobic interactions. I'd like to check the number of H-bonds as a function of time formed by backbone and sidechain, respectively.
I use the standard ptraj script for Hbonds used here
http://ambermd.org/tutorials/basic/tutorial3/section6.htm,
**************************************************************
trajin blah.x
###backbone here
donor mask .O
acceptor mask :GLN.N :GLN.H
acceptor mask :ARG.N :ARG.H
acceptor mask :PHE.N :PHE.H
acceptor mask :TRP.N :TRP.H
acceptor mask :GLU.N :GLU.H
###rest here
#-- Donors from standard amino acids
donor mask :GLN.OE1
donor mask :GLN.NE2
donor mask :GLU.OE1
donor mask :GLU.OE2
#-- Acceptors from standard amino acids
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
acceptor mask :TRP.NE1 :TRP.HE1
acceptor mask :ARG.NH2 :ARG.HH21
acceptor mask :ARG.NH2 :ARG.HH22
acceptor mask :ARG.NH1 :ARG.HH11
acceptor mask :ARG.NH1 :ARG.HH12
acceptor mask :ARG.NE :ARG.HE
hbond distance 3.5 angle 135.0 print 0.25 series hbt out tstrd$p-1.hbd
************************************************************************
The problem arises from different input blah.x. When blah.x includes both beta-sheet, ptraj gives number of Hbonds per strand A. When blah.x only includes one single beta sheet, the number of Hbonds per strand is B. A is smaller than B. This is not as I expected. At least, two runs should give more or less the same results, even though A shoudl be greater than B, including the cross-sheet H-bonds.
What is possibly going on here?
Many thanks.
Binbin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 26 2009 - 10:00:02 PDT
