VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 03 2020 - 16:10:47 CST

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
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