From: M K (mahyar.karimi20_at_gmail.com)
Date: Sun Dec 07 2014 - 22:34:02 CST

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
>
> --
> 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/
>