From: bo liu (
Date: Tue Sep 02 2008 - 10:02:26 CDT

merging a PSF and a PDB? it sounds meaningless...
you really want to do is merging two PDBs and two corresponding PSFs
to contain connectivity information within one file, as Axel has mentioned,
you can try .mol2 format
pdb can be translated into .mol2 format by Open Babel,
connectivity information will be appended automaticly (however may be not
that accurate)

or you can load your pdb file into VMD then use "set bonds" and "get bonds
commands in VMD to generate correct bonds list,
finally, you can write this information into your pdb file as CONECT
you may want to refer to VMD's manual for the usage of the two commands.

Hope it helps,
2008/9/2 Axel Kohlmeyer <>

> On Tue, 2 Sep 2008, wrote:
> MA> Hi,
> MA>
> 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>
> 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.
> cheers,
> axel.
> MA>
> MA> Thanks.
> MA>
> MA> Max
> MA>
> MA>
> MA>
> --
> =======================================================================
> 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.

-Liu bo
Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
Chinese Academy of Sciences, Beijing P.R. China
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