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

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Mon, 11 Aug 2014 21:14:04 +0100

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'

Thanks,
Marc


On 11 August 2014 18:37, Jason Swails <jason.swails.gmail.com> wrote:

> On Mon, 2014-08-11 at 14:40 +0100, Marc van der Kamp wrote:
> > Dear Jason,
> > Thanks for your changes - I think the 'more flexible' PSF parser is a
> good
> > idea.
> > The parameter file in the tarball was made manually, and I clearly made a
> > mistake. I didn't catch this myself before, as I've now been using the
> -str
> > attribute (in chamber and parmed.py's chamber) to pass various additional
> > parameters. I had just used this single file for the test-case. So no
> need
> > to add support for that, I would think.
>
> OK, good :). One other note for ParmEd -- you can pass multiple -param
> and -top flags (whereas with chamber, I think you need 1 param, 1 top,
> and the rest have to be passed as stream files).
>
> ParmEd is actually a bit stricter than chamber when reading stream files
> -- it behaves more like CHARMM (I think), where it looks for commands to
> read a topology section and a parameter section(look for the line "read
> rtf card .app" and "read para card flex @app" in the
> toppar_water_ions.str file bundled with the CHARMM force field, for
> example). Since these command cards don't seem to be found by default
> in parameter and topology files, I don't think you can pass those as
> stream files to the chamber command in ParmEd.
>
> >
> > I'm still having a problem with the test-case with ParmEd (on my
> MacBook),
> > however.
> >
> > I cloned & installed ParmEd fresh from github.
> > I changed the parameter file as you suggested (putting the NBFIX section
> at
> > the end, just before END).
> > What I now get is:
> > > 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 think I see why this is happening, and I've pushed a fix. What I'm
> not exactly sure of is why I wasn't seeing this problem...
>
> Can you see if this works now?
>
> Thanks for helping me work out some of the kinks!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 11 2014 - 13:30:02 PDT
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