From: Biswa Ranjan Meher (
Date: Thu Nov 14 2013 - 17:15:15 CST

Dear VMD developers and Users,

I was trying to save the coordinates from a Desmond trajectory in to PDB
format files using VMD. However, when I checked the VMD generated PDB file,
it surprised me that all the heavy atoms for each residues (except
Hydrogen) are placed together and all the H-atoms for each residues placed
together next.

So, in simple, all the heavy atoms are listed first and then all the
H-atoms are listed next in the PDB file. So, is there anyway to save the
coordinates of all the atoms (heavy + H) of each residue in a sequence

Hope to get a solution.