[AMBER] overestimate hydrogen bonding distance

From: Niko Prasetyo <Niko.Prasetyo.student.uibk.ac.at>
Date: Wed, 20 Feb 2019 10:36:40 +0100

dear all,

I did a hbond analysis for two fragment, caffeine and metacrylic acid
using cpptraj..

here the command that I used

hbond hbond_test out hbond angle 30.0 dist 3.0 donormask :met.O1
donorhmask :met.H5 acceptormask :aff.O1 avgout aaa nointramol series
uuseries bbb

from the hbond analysis, the distance is about 2,7 angstroem and the
angle is 159 degree..

I simply check the distance between these two fragment via VMD, and
the average is should be 1.8 angstroem...

my question is why the hbond distance from cpptraj is much longer?

thank you in advance for the answers,



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Received on Wed Feb 20 2019 - 02:00:03 PST
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