From: bo liu (liubo.njuer_at_gmail.com)
Date: Wed Sep 03 2008 - 00:17:13 CDT

2008/9/2 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>

> 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.

Sure, VMD can do this.

>
>
> 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.

well, if i were in this case, i prefer to edit the pdb file directly with
the bonding information.
i think the only problem is the format. a little bit scripting would solve
the problem.

>
> 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.
>

-- 
-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
Office: (86)-010-88233187
Home: (86)-010-88259765
Cell: 13426057875