On Thu, Aug 7, 2014 at 7:53 AM, Marc van der Kamp <marcvanderkamp.gmail.com>
wrote:
> Hi Jason,
> I don't know yet if ParmEd handles the CGenFF atom types, as I am still
> stuck with the following error (I get similar errors for the test systems,
> CHARMM-style and XPLOR-style psf's alike - see previous email for details):
>
>
> > chamber -top top_all36_prot_ksi.rtf -param par_all36_prot_cgenff_ksi.prm
> -psf ionized.psf -crd ionized.pdb -box bounding
> Creating chamber topology file from PSF ionized.psf, RTF files
> [top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
> Coords from ionized.pdb. Using CMAP. Defining a bounding box. GB Radius set
> mbondi.
> Traceback (most recent call last):
> File "/Users/marcvanderkamp/bin/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/Library/Python/2.7/lib/python/site-packages/ParmedTools/parmed_cmd.py",
> line 141, in _normaldo
> action.execute()
> File
>
> "/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/ParmedTools/ParmedActions.py",
> line 3561, in execute
> parm = ConvertFromPSF(psf, frcfield).view(ChamberParm)
> File
>
> "/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/chemistry/amber/_chamberparm.py",
> line 692, in ConvertFromPSF
> rij = lj_radii[i] + lj_radii[j]
> TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'
>
Ah, it looks like one of the LJ parameters was not set. If these files
are included in the tarball you attached earlier, I will try to reproduce
this problem and make a fix. It would be great getting ParmEd working for
any CHARMM system people have.
>
> As mentioned before, this is probably a consequence of how parmed.py is
>
> installed and my shell environment (?) but any hints on how to solve this
>
> would be greatly appreciated.
>
>
>
> Thanks,
>
> Marc
Thanks!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 07 2014 - 08:30:02 PDT
