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'
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
On 6 August 2014 17:18, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Aug 6, 2014, at 12:06 PM, Marc van der Kamp <marcvanderkamp.gmail.com>
> wrote:
>
> > Dear Robin & Jason,
> >
> > Getting the test psf's in XPLOR format to pass chamber conversion was
> > indeed as simple as using -xpsf instead of -psf to pass the psf file.
> > Apologies for not noting that.
> > I could not pass my original system (with XPLOR format), however; I think
> > this may have to do with the 5+ character atom type names from CGenFF,
> but
> > haven't had the opportunity to test this yet.
> > I will try Sarah's solution when I get the chance - thanks, Sarah.
>
> Does ParmEd handle the 5+ character atom types from CGenFF? (keep in mind
> that the -cmap flag should be deleted from chamber).
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Aug 07 2014 - 05:00:02 PDT
