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'
Best,
Marc
On 12 August 2014 03:37, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Aug 11, 2014 at 4:14 PM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > Hi Jason,
> > Did a git pull and ran setup.py to install (python setup.py install
> --user
> > --install-scripts ~/bin/)
> >
> > Now upon starting parmed.py I immediately get an error:
> >
> > Traceback (most recent call last):
> > File "/Users/marcvanderkamp/Documents/work/ParmEd/parmed.py", line 11,
> in
> > <module>
> > from ParmedTools.logos import Logo
> > File
> > "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/__init__.py",
> line
> > 12, in <module>
> > import ParmedTools.ParmedActions as _PA
> > File
> >
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/ParmedActions.py",
> > line 18, in <module>
> > from ParmedTools.parmlist import ParmList, ChamberParm, AmoebaParm
> > File
> > "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/parmlist.py",
> line
> > 8, in <module>
> > from chemistry.amber.readparm import AmoebaParm
> > File
> >
> "/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/readparm.py",
> > line 26, in <module>
> > from chemistry.amber._amberparm import AmberParm, Rst7
> > File
> >
> >
> "/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/_amberparm.py",
> > line 26, in <module>
> > from chemistry.amber.topologyobjects import (Bond, Angle,
> > File
> >
> >
> "/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/topologyobjects.py",
> > line 20, in <module>
> > from compat24 import all, property
> > File "/Users/marcvanderkamp/Documents/work/ParmEd/compat24.py", line
> 64,
> > in <module>
> > if not hasattr(__builtins__.property, 'setter'):
> > AttributeError: 'dict' object has no attribute 'property'
> >
>
> ​Sorry, this was careless. I was trying to add support for Python 3 to the
> default install process, but it wasn't ready yet. I had meant to move this
> work to a different branch, but forgot to reset my tree before pushing.
> I've reversed that last commit that is causing this problem, and the unit
> tests are passing again.
>
> I'm hopeful that it will work this time. Thanks again for continuing to
> try this for me despite the fact that you've already got it working with
> chamber/ParmEd.
>
> All the best!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 11 2014 - 23:00:02 PDT
