From: Ivan Gregoretti (
Date: Mon May 04 2015 - 22:55:05 CDT

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!