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