VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Sep 02 2008 - 10:46:07 CDT

On Tue, 2 Sep 2008, bo liu wrote:

BL> merging a PSF and a PDB? it sounds meaningless...
BL> you really want to do is merging two PDBs and two corresponding PSFs
BL> respectively?
BL> to contain connectivity information within one file, as Axel has mentioned,
BL> you can try .mol2 format
BL> pdb can be translated into .mol2 format by Open Babel,

no need to use open babel. VMD can write mol2 directly.

BL> connectivity information will be appended automaticly (however may be not
BL> that accurate)
BL>
BL> or you can load your pdb file into VMD then use "set bonds" and "get bonds
BL> commands in VMD to generate correct bonds list,

please re-read max's post. this has already been done.
the point was to have the information from the .pdb file
_and_ the augmented bonding information currently stored
in a .psf file combined into one file.

cheers,
   axel.

BL> finally, you can write this information into your pdb file as CONECT
BL> you may want to refer to VMD's manual for the usage of the two commands.
BL>
BL> Hope it helps,
BL> 2008/9/2 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
BL>
BL> > On Tue, 2 Sep 2008, max_at_liaad.up.pt wrote:
BL> >
BL> > MA> Hi,
BL> > MA>
BL> > MA> I would like to merge two files (one psf and other pdb) into only one
BL> > pdb
BL> > MA> file.
BL> > MA> Actually I load a pdb file into VMD then I change molecule's bonds. So,
BL> > I
BL> > MA> use wirtepdb and writepsf to save the coordinates and bond's
BL> > informations
BL> > MA> respectively.
BL> > MA> So, after this I need to get only one file (a pdb file) with all these
BL> > MA> informations (coordinates and bonds).
BL> >
BL> > hi max,
BL> >
BL> > pdb files don't contain the (forcefield) bonding information.
BL> > please see the documentation of the pdb file format on the
BL> > pdb homepage. there are CONECT records, but they are reserved
BL> > for "unusual bonds" and since VMD as visualization program
BL> > doesn't know anything about chemistry, it cannot determine
BL> > this and doesn't write this.
BL> >
BL> > MA>
BL> > MA> Could anyone help me? Or maybe give another suggestion?
BL> >
BL> > you could try the .mol2 (tripos) file format. that should store
BL> > both connectivity and coordinates. i'm not certain, however, how
BL> > portable that is compared to .pdb.
BL> >
BL> > cheers,
BL> > axel.
BL> >
BL> > MA>
BL> > MA> Thanks.
BL> > MA>
BL> > MA> Max
BL> > MA>
BL> > MA>
BL> > MA>
BL> >
BL> > --
BL> > =======================================================================
BL> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
BL> > Center for Molecular Modeling -- University of Pennsylvania
BL> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
BL> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
BL> > =======================================================================
BL> > If you make something idiot-proof, the universe creates a better idiot.
BL> >
BL>
BL>
BL>
BL> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.