From: John Stone (
Date: Sun Dec 07 2014 - 22:08:43 CST

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.

  John Stone

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           Phone: 217-244-3349