From: Esben A. Gad (eag_at_nano.ku.dk)
Date: Wed Jun 18 2008 - 03:17:04 CDT

Dear vmd-list

I have a 46560 atom solvated system that runs fine for 10 ns in NAMD. I
can load my initial PDB as a new molecule in VMD and then load my DCD into
this molecule. No problem.

However, I'd like to do e.g. interaction energy calculations in VMD, and
for this, I need to load the PSF into VMD.

As I simulate non-protein substrates also, I set up my system with the
Discovery Studio package from Accelrys (which does forcefield typing) and
transfer PSF to NAMD using an in-house script.

When I open VMD and directly try to open my PSF (which, again, runs fine
in NAMD), I get:

--------------------------------------------------------------
vmd > psfplugin) Detected a Charmm31 PSF EXTEnded file
Info) Using plugin psf for structure file
/net/kat.nzcorp.net/z/eq-novovol03/hom
e/esbg/10r/namd/CVS/241APF/protein.psf
Bonds line too short in psf file:
       1 5 2 1 3 1 4 1

ERROR) Error reading bond information.
Info) Analyzing structure ...
Info) Atoms: 46560
Info) Bonds: 0
Info) Residues: 46560
Info) Waters: 0
Info) Segments: 10000
Info) Fragments: 46560 Protein: 0 Nucleic: 0
--------------------------------------------------------------------

As others on this list have discovered, the PSF format is apparently not
trivial to figure out. I have tried to compare my PSF with the examples
given in the file formats appendix of the namd tutorial, but I don't see
any differences compared to the structure of my file. Obviously, the
segments count of 10000 that VMD comes up with is wrong, so it might have
something to do with the way I number my segments?

For anybody interested in helping me debug, I have uploaded my zipped PSF
file (606kb) here:

http://www.fys.ku.dk/~eag/vmd/protein.psf.tar.gz

This problem surprised me, as I thought VMD and NAMD was codeveloped
closely enough to accept the same files. I'd appreciate any help you guys
could come up with.

Thanks, - Esben

-- 
Esben A. Gad
Grad student, Structural Biology & NMR (SBiN) lab
Institute for Molecular Biology
University of Copenhagen