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

From: Jason Swails <>
Date: Sat, 9 Aug 2014 17:16:29 -0400

On Thu, Aug 7, 2014 at 11:58 AM, Marc van der Kamp <
> wrote:

> Hi Jason,
> Perhaps the LJ parameters are the problem, but not the only one... ;)
> FYI, chamber (now working, with the instructions from Sarah earlier in this
> thread) reports:
> --- Found all atom types in topology file
> WARNING: No NONBONDED parameter section in this stream file:
> | /users/chmwvdk/toppar/c36_dec13/top_all36_cgenff.rtf
> WARNING: No NONBONDED parameter section in this stream file:
> | ../RS1.str.txt
> --- Found all nonbond parameters
> I tried to make a 'simple' CGenFF test-case for based on my
> system - just the ligand (with CGenFF atom types) and some water molecules.
> But now I consistently get the following error from
> Action chamber failed
> ChamberError: Problem reading CHARMM PSF
> This is the case with a XPLOR-style and a CHARMM-style psf (with the latter
> including the " 0 0 !NUMLP NUMLPH" line that Sarah indicated
> should be added for chamber compatibility).
> Attached is a tarball with this test system, with:
> dry.rs1.psf - the XPLOR psf
> dry.rs1_charmm.psf - the CHARMM psf
> dry.rs1.pdb - the coordinates

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

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


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Aug 09 2014 - 14:30:03 PDT
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