[AMBER] Hbond analysis

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Wed, 30 Oct 2013 16:34:26 -0200

Hi, I have some doubts related to the hbond analysis results performed
with cpptraj. I have specified the analysis along with the options for
solvent hbond analysis and bridge. Within the hbond between residues, the
interaction between a carboxylate from an asp residue and the hydrogens
from the guanidinium group show up like this:
ASP_204.OD2 ARG_206.HE ARG_206.NE 4228 0.8456
3.0151 145.4176
ASP_204.OD1 ARG_206.HE ARG_206.NE 4072 0.8144
3.2199 154.9778
So, the fraction of frames in which OD2 and OD1 stay bonded to the same
hydrogen atom on arginine is 0.8456 and 0.8144 respectively. How can this
be so? Shouldn’t the fractions add up to 1?
I get even more confused when I take into account the other interactions
that this asp residue does.
ASP_204.OD2 OH1_342.H1 OH1_342.O 4612 0.9224
2.9481 158.4453
This is OD2 bonded to a water molecule bound to a zinc complex.
In the solvent analysis output.
OH1_342.O SolventH SolventDnr 10182 2.0364
2.7305 162.2674
How can the Hbond appear in 10182 frames if I only analysed 5000?
Thank you in advance
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Received on Wed Oct 30 2013 - 12:00:02 PDT
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