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 - 07:30:03 PDT
