VMD-L Mailing List

From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Thu Dec 03 2020 - 10:44:37 CST

Hi Francesco,

If you think that there is a problem with the results generated by the h-bond plugin you can easily check if the distance and angles of some of these bonds are within the ranges selected. You can do that by using the label option of VMD. Just go to Mouse > Label > Bonds and select the two atoms that you think are forming an H-bond. Then go to Mouse > Label > Angles and select the 3 atoms forming this H-bond (D-H-A). By checking the distance and the angle you will see if you should be getting a different result from the plugin.

Best wishes,

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: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thursday, December 3, 2020 at 1:53 AM
To: Rafael Bernardi <rcbernardi_at_auburn.edu>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: [EXTERNAL]Re: vmd-l: h-bond plugin with QMMM

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Hi rafael
Thanks for answering. As a quick replay, attached please see a tga for the last frame of 27M_npt02 QMMM where, as far as I can understand, H-bonds are present, like with all other QMMM that I have carried out
Separately, I'll try to send you the corresponding psf/pdb or/and the avpos.pdb (the averaged pdb from avpos). So that you see where I am misusing the h-bond plugin.
Thanks
francesco

On Wed, Dec 2, 2020 at 7:48 PM Rafael Bernardi <rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>> wrote:
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<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>>
Date: Wednesday, December 2, 2020 at 12:30 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu<mailto: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