PSF file format

Andrew Dalke dalke at ks.uiuc.edu
Sun Jan 11 04:19:05 EST 1998


  Don Bashford <bashford at gage.scripps.edu> pretty much explained
everything, but I want to fill in some minor details.

  The PSF file used by NAMD comes from XPLOR, which is a variation of
the PSF format of CHARMM's.  The NAMD developers (of which I was one)
decided to leave the complications to XPLOR, because it is a hard
problem.  We chose XPLOR because that's what we had in-house.

  Will Ware <wware at world.std.com> asked how to generate a PSF file.
The only way I can suggest to do it is get a copy of XPLOR (or of
CHARMM and write a conversion script; it is a pretty simple
translation).  This isn't a satisfactory answer, but I know of no
freely available program that will do this.  Hint to anyone reading
this;  many people would thank you if you wrote one!

  We were not able to find a good description of the PSF format; we
had to discover it from reverse engineering.  I still don't know what
the last column of the ATOM line describes:

      66 !NATOM
       1 MAIN 1    ACE  CA   CH3E   0.000000E+00   15.0350           0
                                                        This one  ---^

Will also asked a few questions about the h-bond donor/acceptor lines.
For NAMD, those are ignored because the CHARMM force field no longer
depends on it.  Plus, reverse engineering that section of the code was
nasty.

						Andrew
						dalke at mag.com
---
Not speaking for the Molecular Applications Group.



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