Maciej is correct - the distance reported is the donor heavy atom to
acceptor distance (as stated in the manual). I could add an option to
report the H-A distance instead. In the meantime you'd have to
calculate that distance based on the IDs of the atoms involved.
-Dan
On Wed, Feb 20, 2019 at 5:47 AM Niko Prasetyo
<Niko.Prasetyo.student.uibk.ac.at> wrote:
>
> yes, exactly. But I want to measure hydrogen bonding between proton
> and acceptor using cpptraj
>
> Niko
>
> Quoting Maciej Maciejczyk <maciej.maciejczyk.uwm.edu.pl>:
>
> > 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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> >
> > --
> > *******************************************
> > 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
> > *******************************************
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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Received on Mon Feb 25 2019 - 06:00:04 PST
