VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Sun Dec 07 2014 - 21:51:37 CST

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