From: John Stone (
Date: Mon Aug 02 2004 - 09:59:02 CDT

  The errors your getting are because VMD requires all timesteps of
a single molecule to contain the same number of atoms, and when you
try to load them consecutively, it assumes you're trying to load the
second molecule as a new trajectory timestep.

I'd suggest that you try out this script, it attempts to merge
multiple PDB files into a single structure and save it out as a
PDB / PSF pair:

You may need to modify the script in order to use it for your structures,
and I don't believe I've tested it on Windows, though it ought to work.


On Fri, Jul 30, 2004 at 06:30:22PM -0700, Sekwan Oh wrote:
> Dear vmd users,
> I am trying to put two different molecules (with differnt pdb files)
> together and eventually save in a single pdb file for simulation input.
> However it's not easy to do so when I tried to load one pdb first and load
> the second file using "Load Data into Molecule..".
> This gives error messages such as
> ERROR>Error reading optional structure information from coordinate file
> C:/........***.pdb
> ERROR> Incorrect number of atoms <2> in
> ERROR> coordinate file C:/..........***.pdb
> Any suggestion?
> Plus, is coordinate of the molecule changed by moving, rotating and etc.?
> Because I want "the coordinate of the first pdb file remain the same" and
> "the coord of the second pdb changed" so that I can have single
> concatenated pdb file with two molecules.
> I appologize if the questions are too naive, but any help and guidance
> would be greatly appreciated.
> Thank you so much.
> Truly Yours,
> Sekwan
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