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).
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Received on Wed Jun 12 2019 - 10:30:02 PDT
