Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)

From: Marc van der Kamp <>
Date: Sun, 10 Aug 2014 22:05:36 +0100

On 9 August 2014 22:16, Jason Swails <> wrote:

> ​Where did this PSF file come from?

PSF is written by VMD's psfgen, version 1.5 I think.

> It's missing 3 sections that I haven't
> seen ​_all_ missing from a PSF file: NUMLP/NUMLPH, and NCRTERM (effectively
> the CMAP section).

NCRTERM is expected not to be there (or at least unpopulated) in this case,
as the test-case was without protein (just CGenFF parameterized ligand and
some water).
psfgen does write this section (as it should) when protein (and thus CMAP
terms) are present. But I'm assuming old (pre-CMAP) charmm versions will
also not write this section.

As Sarah pointed out already in this thread, when you do "writepsf charmm
<mypsf>.psf" in psfgen, the following line is 'missing' (but required by
     0 0 !NUMLP NUMLPH

> If this is a typical example from a standard source, I
> will probably have to rethink how I parse PSF files in ParmEd to be a bit
> more flexible to the abuse the PSF file format has taken (reminiscent of
> what's happened to the PDB format, really...

I'd say psfgen is reasonably standard, as it is the main option to write
psf's if you don't have access to or don't want to use charmm.

> It may be worth doing that, anyway. Thanks for the report.
> Jason

Thanks for all your hard work!

> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
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Received on Sun Aug 10 2014 - 14:30:02 PDT
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