VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Dec 08 2014 - 01:49:11 CST

In VMD the first letter indicates the element. So a capital H would sign an atom as hydrogen.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von M K
Gesendet: Montag, 8. Dezember 2014 05:34
An: John Stone; M K; vmd-l_at_ks.uiuc.edu
Betreff: Re: vmd-l: H-Bonds not shown when loading by topo readlammpsdata

 

Thank you for the quick reply.

No, it does not recognize. But through Keywords: Name or type , I know which atoms are hydrogen.

Can you please explain more how I can set the atom names for recognizing H-bonds?

 

On Mon, Dec 8, 2014 at 3:08 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

Does VMD recognize the hydrogens in your system? If not, then
the issue is probably as simple as just getting the atom names
set so VMD knows what they are.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 08, 2014 at 02:51:37PM +1100, M K wrote:
> I have made a lammps data file using msi2lmp tool of lammps. When I load
> this data file using " topo readlammpsdata " and then load the trajectory
> files into it in vmd, I cannot see the H-bonds when selecting Drawing
> Method: "Hbond" .
> I couldn't load a pdb file, since my structure has more that 9999 residues
> and Mat Studio cannot save it as a pdb file.
>
> Do you have any suggestion I can:
> 1- have a good pdb file to load in vmd initially;
> 2- see and calculate the H-bonds in VMD?
>
> Thank you 

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