VMD-L Mailing List

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Dec 03 2020 - 15:52:18 CST

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
>>
>>