Try installing the latest version of AmberTools (18). I believe this error
was fixed then.
Thanks,
Jason
On Wed, Jul 25, 2018 at 12:10 AM, Suzan Bose <bosesuzan143.gmail.com> wrote:
> Dear all,
> I am a beginner of this amber field. I have installed amber16. I want to
> convert my charmm force field to amber format by the chamber module which
> is incorporated into the parmed, but unable to do. The error is as follows:
> ###################################################################
> ParmEd: a Parameter file Editor
> Reading input from STDIN...
> > chamber -top top_all22_prot.rtf -param par_all22_prot.prm -str
> toppar_water_ions.str -psf A.psf -crd A.pdb
> Creating chamber topology file from PSF A.psf, RTF files
> [top_all22_prot.rtf], PAR files [par_all22_prot.prm], and STR files
> [toppar_water_ions.str]. Coords from A.pdb. Using CMAP. GB Radius set
> mbondi.
> Unexpected failure:
> TypeError: 'str' object does not support item assignment
>
> Traceback is
>
> File
> "/data/apps/amber16/lib/python2.7/site-packages/
> parmed/tools/parmed_cmd.py",
> line 159, in _normaldo
> action.execute()
> File
> "/data/apps/amber16/lib/python2.7/site-packages/parmed/tools/actions.py",
> line 3883, in execute
> parmset.read_parameter_file(pfile)
> File
> "/data/apps/amber16/lib/python2.7/site-packages/
> parmed/charmm/parameters.py",
> line 415, in read_parameter_file
> elem = elem.lower(); elem[0] = elem[0].upper()
> #########################################################################
>
> Help me to get rid of this problem.
> Any comments/suggestions will be appreciated.
>
> Thanks,
> Suzan
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Thu Jul 26 2018 - 10:30:02 PDT
