Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Tue, 12 Aug 2014 13:43:11 +0100

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'
> >
>
> ‚ÄčI'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.

Thanks,
Marc
PS I made the same modification in the parameter file, i.e move NBFIX
section to the end. I also unpacked the tarball again and made the same
modification, just to make sure the same files are used.
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Received on Tue Aug 12 2014 - 06:00:02 PDT
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