I think that cpptraj returns distance between heavy atoms and you
probably measure distance between proton and acceptor in VMD
MM
On 20.02.2019 10:36, Niko Prasetyo wrote:
> 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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--
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Maciej S. Maciejczyk, PhD
Division of Physics and Biophysics
Faculty of Food Sciences
University of Warmia and Mazury in Olsztyn
ul. Oczapowskiego 4
10-719 Olsztyn
Poland
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Received on Wed Feb 20 2019 - 02:30:02 PST
