AMBER Archive (2009)

Subject: [AMBER] contradictive hydrogen bonds using ptraj

From: Binbin Liu (B.B.Liu_at_leeds.ac.uk)
Date: Mon Oct 26 2009 - 11:42:20 CDT

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_at_N :GLN_at_H
acceptor mask :ARG_at_N :ARG_at_H
acceptor mask :PHE_at_N :PHE_at_H
acceptor mask :TRP_at_N :TRP_at_H
acceptor mask :GLU_at_N :GLU_at_H
###rest here
#-- Donors from standard amino acids
donor mask :GLN_at_OE1
donor mask :GLN_at_NE2
donor mask :GLU_at_OE1
donor mask :GLU_at_OE2
#-- Acceptors from standard amino acids
acceptor mask :GLN_at_NE2 :GLN_at_HE21
acceptor mask :GLN_at_NE2 :GLN_at_HE22
acceptor mask :TRP_at_NE1 :TRP_at_HE1
acceptor mask :ARG_at_NH2 :ARG_at_HH21
acceptor mask :ARG_at_NH2 :ARG_at_HH22
acceptor mask :ARG_at_NH1 :ARG_at_HH11
acceptor mask :ARG_at_NH1 :ARG_at_HH12
acceptor mask :ARG_at_NE :ARG_at_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

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