Just to follow up for posterity, after examining the files the issue
was a misunderstanding of how the hydrogen bond angle is determined.
Cpptraj determines hydrogen bonds like so:
D-H ... A
Where D is the heavy atom donor, H is the donor hydrogen, and A is the
heavy atom acceptor. The distance is D to A, and the angle is D - H -
A. OP had been using a different atom order for the angle calculation,
hence the confusion.
TL;DR - the cpptraj hbond calculation is ok.
-Dan
On Wed, Jun 12, 2019 at 1:22 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Would it be possible for you to send me off-list files I can use to
> reproduce this issue? Thanks,
>
> -Dan
>
> On Wed, Jun 12, 2019 at 12:14 PM Stefano Motta <stefano.motta.unimib.it> wrote:
> >
> > Dear amber community,
> >
> > I'm using cpptraj to compute the H-bond between water and a ammine group.
> > I'm interested in the H-bond with water as a donor, an the nitrogen as
> > acceptor: O-H---N
> > I'm using the following cpptraj commands:
> >
> > trajin prod.center.nc
> > > hbond All solventdonor :WAT acceptormask @N1 dist 3.5 angle 150
> > > create AMBER_hbond.agr All[UV]
> > > run
> >
> >
> > the trajectory is already imaged; N1 is the atom name of the nitrogen (the
> > only nitrogen in the system).
> > The problem is that visually inspect with VMD, I have some frames where the
> > geometric criteria are satisfied for more water molecules than what cpptraj
> > find (distance lower than 3.5Å and angle greater than 150°).
> > Interestingly if I'll do the hbond calculation with the VMD plugin with the
> > same geometric criteria (in that case distance lower 3.5 and angle lower
> > than 30) I obtain exactly the same results. On the contrary if I use the
> > gmx hbond command of gromacs with the same geometric criteria the number of
> > H-bond found is higher and correspond to what I see in VMD. What am I doing
> > wrong?
> >
> > Thanks to all,
> > Stefano
> >
> >
> >
> > --
> > ________________________________________________________________
> >
> > Stefano Motta PhD
> >
> > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
> >
> > Università degli Studi di Milano Bicocca
> > Department of Earth and Environmental Sciences
> >
> > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > _________________________________________________________________
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Jun 13 2019 - 07:00:02 PDT
