Dear Amber users,
I am doing hydrogen bond analysis with cpptraj. I want to analyze the hydrogen bond between interacting residues of protein-protein complexes:
hbond Backbone :19,20,21,69,142,163,190,252,286,258,287,264,312 nointramol avgout BB.avg.dat series uuseries bbhbond.xvg
create nhbvtime.agr Backbone[UU]
rms BBrmsd :19,20,21,69,142,163,190,252,286,258,287,264,312 out BBrmsd.agr
run
lifetime Backbone[solutehb] out backbone.lifetime.xvg
runanalysis
As result, I was expecting a total of 11 hydrogen bonds, but analyzing the backbone.lifetime.xvg file I got extra interactions, for instance for the residues GLU142 and LYS264 (I was expecting 2 hbond):
GLU_142.OE1-LYS_264.NZ-HZ1
GLU_142.OE2-LYS_264.NZ-HZ1
GLU_142.OE1-LYS_264.NZ-HZ2
GLU_142.OE2-LYS_264.NZ-HZ2
GLU_142.OE1-LYS_264.NZ-HZ3
GLU_142.OE2-LYS_264.NZ-HZ3
I can't understand this result. Can anyone help me with that?
Regards
Nubia
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Received on Fri Feb 16 2018 - 14:00:03 PST
