VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 20 2008 - 09:57:37 CDT

On Fri, 20 Jun 2008, Esben A. Gad wrote:

esben,

is there a specific reason why you are using the EXT form of PSF?
it might have been easier to just try removing the EXT than fixing
the whole output.

[...]

to check the format, you can either read the psf molfile
reader comments and/or have a look at the example files
in the VMD public biocore project under testfiles/psf/charmm31

cheers,
   axel.

EG>
EG> My psf i still here:
EG> http://www.fys.ku.dk/~eag/vmd/protein.psf.tar.gz
EG>
EG> Thanks, - Esben
EG>
EG>
EG> ------------Old Msg--------------------------------------------
EG> Hi Esben,
EG>
EG> from the psf reader in vmd:
EG>
EG> /* Check that there is enough space in the line we are about to
EG> read */
EG> if (nbond-i >= 4) {
EG> if(charmmext == 1) minlinesize = 20*4 ; else minlinesize = 16*4;
EG> } else {
EG> if(charmmext == 1) minlinesize = 20*(nbond-i); else minlinesize
EG> = 16*(nbond-i);
EG> }
EG> if (strlen(inbuf) < minlinesize) {
EG> fprintf(stderr, "Bonds line too short in psf file: \n%s\n", inbuf);
EG> break;
EG> }
EG>
EG> Since you've flagged your psf as an extended psf, you need to have
EG> fields that are 10 characters wide instead of 8 (see
EG> http://www.charmm.org/package/changelogs/c31log.html). NAMD is less
EG> picky about this, but technically vmd is right to insist.
EG>
EG> Best,
EG> Peter
EG>
EG> Esben A. Gad wrote:
EG> > Dear vmd-list
EG> >
EG> > I have a 46560 atom solvated system that runs fine for 10 ns in NAMD. I
EG> > can load my initial PDB as a new molecule in VMD and then load my DCD into
EG> > this molecule. No problem.
EG> >
EG> > However, I'd like to do e.g. interaction energy calculations in VMD, and
EG> > for this, I need to load the PSF into VMD.
EG> >
EG> > As I simulate non-protein substrates also, I set up my system with the
EG> > Discovery Studio package from Accelrys (which does forcefield typing) and
EG> > transfer PSF to NAMD using an in-house script.
EG> >
EG> > When I open VMD and directly try to open my PSF (which, again, runs fine
EG> > in NAMD), I get:
EG> >
EG> > --------------------------------------------------------------
EG> > vmd > psfplugin) Detected a Charmm31 PSF EXTEnded file
EG> > Info) Using plugin psf for structure file
EG> > /net/kat.nzcorp.net/z/eq-novovol03/hom
EG> > e/esbg/10r/namd/CVS/241APF/protein.psf
EG> > Bonds line too short in psf file:
EG> > 1 5 2 1 3 1 4 1
EG> >
EG> > ERROR) Error reading bond information.
EG> > Info) Analyzing structure ...
EG> > Info) Atoms: 46560
EG> > Info) Bonds: 0
EG> > Info) Residues: 46560
EG> > Info) Waters: 0
EG> > Info) Segments: 10000
EG> > Info) Fragments: 46560 Protein: 0 Nucleic: 0
EG> > --------------------------------------------------------------------
EG> >
EG> > As others on this list have discovered, the PSF format is apparently not
EG> > trivial to figure out. I have tried to compare my PSF with the examples
EG> > given in the file formats appendix of the namd tutorial, but I don't see
EG> > any differences compared to the structure of my file. Obviously, the
EG> > segments count of 10000 that VMD comes up with is wrong, so it might have
EG> > something to do with the way I number my segments?
EG> >
EG> > For anybody interested in helping me debug, I have uploaded my zipped PSF
EG> > file (606kb) here:
EG> >
EG> > http://www.fys.ku.dk/~eag/vmd/protein.psf.tar.gz
EG> >
EG> > This problem surprised me, as I thought VMD and NAMD was codeveloped
EG> > closely enough to accept the same files. I'd appreciate any help you guys
EG> > could come up with.
EG> >
EG> > Thanks, - Esben
EG>
EG> 

-- 
=======================================================================
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
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