PSF file format

Will Ware wware-nospam at
Wed Jan 7 09:07:41 EST 1998

I have been starting to get acquainted with the NAMD modeling package,
and I hope somebody patient will be willing to answer what are probably
some very basic questions. I see that in the sample data for NAMD,
there are four files (alanin (a NAMD script), alanin.pdb, alanin.params,
and alanin.psf). I am clear on the first three files, and I can understand
most of what's going on with the psf file, but there are a few things in
it that I don't understand. Here is a short segment of it:

      66 !NATOM
       1 MAIN 1    ACE  CA   CH3E   0.000000E+00   15.0350           0
       2 MAIN 1    ACE  C    C      0.450000       12.0110           0
       3 MAIN 1    ACE  O    O     -0.450000       15.9994           0
       4 MAIN 2    ALA  N    NH1   -0.350000       14.0067           0
       5 MAIN 2    ALA  H    H      0.250000       1.00800           0
       6 MAIN 2    ALA  CA   CH1E   0.100000       13.0190           0
       7 MAIN 2    ALA  CB   CH3E   0.000000E+00   15.0350           0

It's clear that the numbers over here ---------------/\  are masses, and
I can see that the CA and CB notations are used to represent small clumps
of carbons and hydrogens. What are ----/\  these numbers? My best guess
is that they are fractional electric charges due to electron imbalances in
covalent bonds, have I got that right? And if so, would I be correct in
guessing that they are fractions of a proton charge?

Later in the file, there are a couple of sections for "donors" and
"acceptors". I'm guessing this is probably a really dumb question, but
what is being donated and accepted? Donors always seem to be hydrogens
and nitrogens, and acceptors seem to be lone carbons and oxygens. I've
done a little reading about molecular mechanics modeling and I'm not
clear what acceptors and donors are in this context, and how they are
involved with modeled interatomic forces.

My last question is, where does the PSF file come from? It looks like it
is derived from the PDB file. I can imagine a program that reads in the
PDB file, figures out bonds based on interatomic distances, and then
enumerates which bond, angle, dihedral, and improper energy terms are
needed to model it, along with the other stuff in the file. If that's
the case, where do I find the software to generate the PSF file? It
doesn't seem to have come with the NAMD program.

Thanks for any answers anybody can provide for these questions.
   People say that everyone has a few skeletons in their closet.  Not me.
   Well, not yet anyway.  I mean, the bodies are still decomposing.
Will Ware		email: wware[at]world[dot]std[dot]com

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