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

From: Jason Swails <>
Date: Mon, 11 Aug 2014 13:37:48 -0400

On Mon, 2014-08-11 at 14:40 +0100, Marc van der Kamp wrote:
> Dear Jason,
> Thanks for your changes - I think the 'more flexible' PSF parser is a good
> idea.
> The parameter file in the tarball was made manually, and I clearly made a
> mistake. I didn't catch this myself before, as I've now been using the -str
> attribute (in chamber and's chamber) to pass various additional
> parameters. I had just used this single file for the test-case. So no need
> to add support for that, I would think.

OK, good :). One other note for ParmEd -- you can pass multiple -param
and -top flags (whereas with chamber, I think you need 1 param, 1 top,
and the rest have to be passed as stream files).

ParmEd is actually a bit stricter than chamber when reading stream files
-- it behaves more like CHARMM (I think), where it looks for commands to
read a topology section and a parameter section(look for the line "read
rtf card .app" and "read para card flex @app" in the
toppar_water_ions.str file bundled with the CHARMM force field, for
example). Since these command cards don't seem to be found by default
in parameter and topology files, I don't think you can pass those as
stream files to the chamber command in ParmEd.

> I'm still having a problem with the test-case with ParmEd (on my MacBook),
> however.
> I cloned & installed ParmEd fresh from github.
> I changed the parameter file as you suggested (putting the NBFIX section at
> the end, just before END).
> What I now get is:
> > chamber -top top_all36_prot_ksi.rtf -param par_all36_prot_cgenff_ksi.prm
> -psf dry.rs1_charmm.psf -crd dry.rs1.pdb
> Creating chamber topology file from PSF dry.rs1_charmm.psf, RTF files
> [top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
> Coords from dry.rs1.pdb. Using CMAP. GB Radius set mbondi.
> Traceback (most recent call last):
> File "/Users/marcvanderkamp/Documents/work/ParmEd/", line 161,
> in <module>
> parmed_commands.cmdloop()
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/",
> line 142, in cmdloop
> stop = self.onecmd(line)
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/",
> line 221, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/",
> line 141, in _normaldo
> action.execute()
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/",
> line 3563, in execute
> parm.load_coordinates(coords)
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/",
> line 940, in load_coordinates
> for i, atom in enumerate(self.atom_list):
> AttributeError: 'ChamberParm' object has no attribute 'atom_list'

I think I see why this is happening, and I've pushed a fix. What I'm
not exactly sure of is why I wasn't seeing this problem...

Can you see if this works now?

Thanks for helping me work out some of the kinks!

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 11 2014 - 11:00:02 PDT
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