Thanks Jason!
No crying necessary - it works fine for me now too!
Best wishes,
Marc
On 12 August 2014 15:16, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Aug 12, 2014 at 8:43 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > Hi Jason,
> >
> > On 12 August 2014 12:52, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > > 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...
> > >
> > > Yes, I am almost certain this is where the problems/errors stem from.
> > I installed parmed as follows:
> > $ pwd
> > /Users/marcvanderkamp/Documents/work/
> > $ rm -rf ParmEd
> > $ git clone https://github.com/swails/ParmEd.git
> > $ cd ParmEd
> > $ python setup.py install --user --install-scripts ~/bin/
> >
> > I've now also tried to do the same directly in ~/
> > This leads to the same errors. So it must be to do with how python looks
> up
> > the modules? Not sure what I should do to fix this.
> >
>
> OK, I think I solved the problem. When OpenMM is installed on your
> system, ParmEd loads the OpenMM-enabled prmtop classes by default to allow
> you to leverage OMM's capabilities directly in ParmEd (like computing
> energies, running simulations, etc.). So on my machine, the ChamberParm
> class created by chamber was cast to an OpenMMChamberParm class, and that
> casting provided the required attributes (like atom_list).
>
> Since you don't have OpenMM installed, that cast did not occur and you got
> the error you observed (that's the challenge with supporting the
> flexibility of having numerous packages being optional rather than
> required). I've fixed this error (which I was able to reproduce when
> removing OMM from my PYTHONPATH) and it now works fine for me. If it
> _still_ doesn't work for you I think I'm going to cry.
>
> Thanks again,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Aug 12 2014 - 09:30:02 PDT
