On Thu, Aug 14, 2014 at 12:31 PM, Sarah Witzke <witzke.sdu.dk> wrote:
> Hi Jason,
>
> I have downloaded the latest ParmEd from your github (just a couple of
> hours ago) and done "python setup.py build", "python setup.py install".
> When I run ParmEd I give the full path to this executable to make sure I
> use this version.
> I have a pdb and a psf file of a membrane containing POPC and ergosterol
> from the charmm-membrane-builder-gui. When I try to use chamber in ParmEd
> with this command:
> *****
> chamber -top top_all36_lipid.rtf -top top_all36_cgenff.rtf -param
> par_all36_lipid.prm -param par_all36_cgenff.prm -str
> toppar_all36_lipid_cholesterol.str -str toppar_water_ions.str -psf
> step5_assembly.psf -crd step5_assembly.pdb -box 72.5,72.5,82 -nocmap
> *****
> I get this error:
> *****
> Creating chamber topology file from PSF step5_assembly.psf, RTF files
> [top_all36_lipid.rtf, top_all36_cgenff.rtf], PAR files
> [par_all36_lipid.prm, par_all36_cgenff.prm], and STR files
> [toppar_all36_lipid_cholesterol.str, toppar_water_ions.str]. Coords from
> step5_assembly.pdb. NO CMAP. Box info [72.5, 72.5, 82.0, 90.0, 90.0, 90.0].
> GB Radius set mbondi.
> Traceback (most recent call last):
> File "/Users/witzke/ParmEd-1.1/parmed.py", line 161, in <module>
> parmed_commands.cmdloop()
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 142, in cmdloop
> stop = self.onecmd(line)
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 219, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File "/Users/witzke/ParmEd-1.1/ParmedTools/parmed_cmd.py", line 141, in
> _normaldo
> action.execute()
> File "/Users/witzke/ParmEd-1.1/ParmedTools/ParmedActions.py", line 3563,
> in execute
> parm.load_coordinates(coords)
> File "/Users/witzke/ParmEd-1.1/chemistry/amber/_amberparm.py", line 940,
> in load_coordinates
> for i, atom in enumerate(self.atom_list):
> AttributeError: 'ChamberParm' object has no attribute 'atom_list'
> *****
>
> It seems similar to en error Marc had previously but I can't figure out
> what I should do differently. Do you have an idea?
>
Did you clone the repository or download one of the releases? You need to
clone the repo to get a working chamber action. I'm in the middle of
something that is preventing me from issuing another release (hopefully
done in a week or so).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 14 2014 - 10:00:03 PDT
