From: Axel Kohlmeyer (
Date: Tue Sep 02 2008 - 08:15:39 CDT

On Tue, 2 Sep 2008, wrote:

MA> Hi,
MA> I would like to merge two files (one psf and other pdb) into only one pdb
MA> file.
MA> Actually I load a pdb file into VMD then I change molecule's bonds. So, I
MA> use wirtepdb and writepsf to save the coordinates and bond's informations
MA> respectively.
MA> So, after this I need to get only one file (a pdb file) with all these
MA> informations (coordinates and bonds).

hi max,

pdb files don't contain the (forcefield) bonding information.
please see the documentation of the pdb file format on the
pdb homepage. there are CONECT records, but they are reserved
for "unusual bonds" and since VMD as visualization program
doesn't know anything about chemistry, it cannot determine
this and doesn't write this.

MA> Could anyone help me? Or maybe give another suggestion?

you could try the .mol2 (tripos) file format. that should store
both connectivity and coordinates. i'm not certain, however, how
portable that is compared to .pdb.


MA> Thanks.
MA> Max

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.