VMD-L Mailing List

From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Wed Dec 02 2020 - 12:48:28 CST

Hello Francesco,

I am going to need more details to understand what you are doing.

However, I just want to point out that there is no difference in how this particular plugin will work with an MD trajectory coming from a QM, QM/MM, or MM calculation.
If you are loading a trajectory file with only the QM atoms, which seems to be the case, you might not have any H-bonds present. That can easily happen if your QM system is very small.

Best,

Rafael


……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
www.ks.uiuc.edu/~rcbernardi<http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393





From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <chiendarret_at_gmail.com>
Date: Wednesday, December 2, 2020 at 12:30 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: h-bond plugin with QMMM

Hello
I am trying to use the 1.9.3 VMD h-bond plugin. No problem with protein MD trajectories while empty Multiplot with QMonly (implicit solvent) psf/dcd trajectories for the same proteins even by increasing distances and angles.
Why that?
Thanks for advice
francesco pietra