VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 03 2020 - 23:14:09 CST

Thanks JC, I just thought we ought to ask the man who actually knows ;-)

Best,
  John

On Fri, Dec 04, 2020 at 01:11:14AM +0000, Gumbart, JC wrote:
> Called me out!
>
> The names are only there if you want to limit selections to traditionally polar atoms (N, O, S, F). Otherwise, the plugin is just a wrapper on the ???measure hbonds??? command. As long as the ???Only polar atoms (N, O, S, F)???? box is UNchecked, the output should be the same as what one could get visually (I???m pretty sure VMD uses the same internal logic for the ???measure hbonds??? command and the hbonds representation).
>
> Best,
> JC
>
> > On Dec 3, 2020, at 5:10 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > JC Gumbart wrote the hbonds plugin originally, so hopefully he can
> > answer any and all details you're after. Looking at the code very quickly,
> > I do see a few places where it's looking for specific atom names, so indeed,
> > atom naming may need to match its expectations.
> >
> > Best regards,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Dec 03, 2020 at 04:52:18PM -0500, Marcelo C. R. Melo wrote:
> >> Hi all,
> >> I don't remember using this particular plugin before, so this question is
> >> to you and anyone else who may have some knowledge of this code:
> >> Could it be that the code does not know that your ligand has donors or
> >> acceptors for the H-bonds? Or is the plugin just looking for atom names
> >> ("O", "N", etc), regardless of residue name?
> >> I am wondering if atom or residue naming could be the issue here, since you
> >> mentioned you already manually checked the distances and angles.
> >> Best,
> >> Marcelo
> >>
> >> On Thu, 3 Dec 2020 at 15:14, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> >>
> >>> 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
> >>>>
> >>>>
> >
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
> >
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/