From: Daniel Möller (
Date: Tue May 05 2015 - 02:13:30 CDT


there is a simple method:
- load your pdb as a "new molecule" as much you need for the final
- move every molecule with "Mouse -> Move -> Molecule" to another position
- save the new position "File -> Save coordinate" in a new file (or a temp-file)
- copy-paste every structure in one pdb via a text editor, but between every molecule should be a "TER"
(pay attention to the empty space at the end of the lines in your pdbs, so you don't corrupt your pdb-structure. See Ivans link for standard pdb format)

I hope this helps


Daniel Möller

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von Ivan Gregoretti
Gesendet: Dienstag, 5. Mai 2015 05:55
An: 丁晗
Cc: vmd-l
Betreff: Re: vmd-l: How to create an aggregation of molecules with VMD?

Hello dingh09,

Yes, multiple molecules are common in a single PDB files.

For example, see the antibody structure 4NZU:

In that file, "CHAIN: L" is the light chain poly-peptide and the
"CHAIN: H" is the heavy chain poly-peptide.

Likewise, any co-crystal structure implies at least two molecules. The are plenty of co-crystals at RCSB.

A solvated structure is yet another example of multiple molecules in a single PDB file. Granted that water is a small molecule but it is still a molecule. ;)

For more on the PDB standard, see
In particular, look for section COMPND and look at the first and second examples.

I hope this helps.


On Mon, May 4, 2015 at 11:12 PM, 丁晗 <> wrote:
> Hi,
> I want to create an aggregation of benzene with VMD, so that I can
> solvate them in water box and monitor the solvation process. However,
> I can create only one molecule with molefacture. So is there any way
> to create multiple molecules in one pdb file?
> thank you!