From: Josh Vermaas (
Date: Wed Feb 19 2014 - 00:18:03 CST

Hi Chetan,

PDB and PSF files are one-indexed, but "index" as something in VMD is
zero-indexed. Thus the first atom in the PDB file has index 0, not 1.
Try "serial" instead, which is one-indexed. "serial 1" gives you the
first atom in the pdb, not the second like "index 1" does.
-Josh Vermaas

On 2/18/14, 7:18 PM, Chetan Mahajan wrote:
> Hi,
> I open .gro file in VMD, move the residues I want to particular
> position and then save coordinates in .pdb file. Now, if I pick
> certain atoms using VMD tool, i get their description such as atom
> index and coordinates. However, the corresponding .pdb file has the
> atoms with same index, but different coordinates. Why are the visual
> and in-file coordinates not matching up?
> Thanks
> Chetan