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 - 09:30:02 PDT
