From: John Stone (
Date: Fri Nov 22 2013 - 23:38:10 CST

  VMD will write the atoms to a PDB file with the ordering
preserved from whatever file you originally loaded. If you expect
the ordering of the atoms to be rearranged in some way, you will
need to do this with your own scripts, likely by creating a new
molecule via "mol new atoms" and setting all of the atom data
in your own script, followed by use of "mol reanalyze". Short of
reordering the atoms with your own script, VMD will always write out
the molecule with the atoms ordered the same way they were originally

  John Stone

On Thu, Nov 14, 2013 at 06:15:15PM -0500, Biswa Ranjan Meher wrote:
> 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
> chronology.
> Hope to get a solution.
> Thanks
> Biswa

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