On Tue, Aug 12, 2014 at 1:50 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Thanks Jason - No problem for the testing, it's in my benefit too! (a
> workflow with just needing one pass through ParmEd is preferable!).
> Anyway, I got the following error now:
>
> > 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/parmed.py", line 161,
> in <module>
> parmed_commands.cmdloop()
> File
>
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 142, in cmdloop
> stop = self.onecmd(line)
> File
>
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 221, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/parmed_cmd.py",
> line 141, in _normaldo
> action.execute()
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/ParmedActions.py",
> line 3563, in execute
> parm.load_coordinates(coords)
> File
>
> "/Users/marcvanderkamp/Documents/work/ParmEd/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'
>
I'm at a complete loss here. It works fine for me and I can't possibly
see how you are getting these errors (and I'm not).
One thing that's a little concerning is that you've installed ParmEd, yet
the modules that it is using still seem to come from your source code
folder and not from
/home/marcvanderkamp/Library/Python/2.7/lib/python/site-packages...
Also, I'm not sure that I have the exact files you're using. I'm still
using the files from test_cgenff.tgz that you attached to an earlier
message. If I use the files as-is, I get this error:
File
"/Users/swails/Library/Python/2.7/lib/python/site-packages/ParmedTools/ParmedActions.py",
line 3561, in execute
parm = ConvertFromPSF(psf, frcfield).view(ChamberParm)
File
"/Users/swails/Library/Python/2.7/lib/python/site-packages/chemistry/amber/_chamberparm.py",
line 691, in
ConvertFromPSF
rij = lj_radii[i] + lj_radii[j]
TypeError: unsupported operand type(s) for +: 'NoneType' and 'NoneType'
which is a result of the parameter file being malformed. If I fix the prm
file (by putting the NBFIX section at the end), I get the following:
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.
Outputting Amber topology file test.parm7 and restart test.rst7
Done!
which indicates everything worked (I've attached the test.parm7 and
test.rst7 files here). But until I can reproduce the errors you're seeing,
I don't know how I can fix it...
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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- application/octet-stream attachment: test.rst7
Received on Tue Aug 12 2014 - 05:00:02 PDT
