VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 03 2020 - 13:44:20 CST

Hi Rafael
I had alredy done that for the files that I sent you and other ones. Even
when distances and angles suggest H-bonding the plugin, in ny hands, does
not reveal any H- bond.
All the best
francesco

On Thu, Dec 3, 2020, 17:44 Rafael Bernardi <rcbernardi_at_auburn.edu> wrote:

> 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
>
> rcbernardi_at_ks.uiuc.edu
>
> 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
>
>
>
> *NOTICE: This email originated from Gmail. Please report any phishing
> activity to phishing_at_auburn.edu <phishing_at_auburn.edu>.*
>
> 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>
> 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
>
> rcbernardi_at_ks.uiuc.edu
>
> 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
>
>