Dear Jason,
Thanks a lot for your detailed reply. I just switched to the
github.com/ParmEd/ParmEd repository.
And with the charmm c36_aug14 (I may have used an earlier version
previously) parameter files:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_aug14.tgz
the following command works fine for me now:
chamber -param par_all36_prot.prm -param par_all36_lipid.prm -param
par_all36_cgenff.prm -str toppar_water_ions.str -psf
4mqs-apo-pro-mem-wb-0.0M.psf -crd 4mqs-apo-pro-mem-wb-0.0M.pdb
cheers,
Yinglong
On Wed, May 6, 2015 at 6:59 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, May 6, 2015 at 12:42 PM, Yinglong Miao <yinglong.miao.gmail.com>
> wrote:
>
> > Dear All,
> >
> > I have been trying to convert vmd-generated psf/pdb files for a
> > membrane-protein system using newly installed parmed.py from
> > https://github.com/swails/ParmEd.git. I think I have the latest topology
> > and parameter files, but keep getting the following error message:
> >
>
> Just as a pointer; this link points to my personal fork of the ParmEd
> repository. Instead, try github.com/ParmEd/ParmEd (or just download and
> install the latest AmberTools 15 distribution).
>
>
>
> > > chamber -top top_all36_prot.rtf -top top_all36_lipid.rtf -top
> > top_all36_cgenff.rtf -param par_all36_prot.prm -param par_all36_lipid.prm
> > -param toppar_water_ions.str -psf 4mqs-apo-pro-mem-wb-0.0M.psf -crd
> > 4mqs-apo-pro-mem-wb-0.0M.pdb
> >
>
> ParmEd knows the difference between parameter files, topology files, and
> stream files. Try using "-str" to specify stream files instead of -param.
>
>
>
> > Creating chamber topology file from PSF 4mqs-apo-pro-mem-wb-0.0M.psf, RTF
> > files [top_all36_prot.rtf, top_all36_lipid.rtf, top_all36_cgenff.rtf],
> and
> > PAR files [par_all36_prot.prm, par_all36_lipid.prm,
> toppar_water_ions.str]
> > Coords from 4mqs-apo-pro-mem-wb-0.0M.pdb. Using CMAP. GB Radius set
> mbondi.
> > Traceback (most recent call last):
> > File "/net/home/ymiao/bin/parmed.py", line 183, in <module>
> > parmed_commands.cmdloop()
> > File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
> > stop = self.onecmd(line)
> > File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
> > return func(arg)
> > File "<string>", line 1, in <lambda>
> > File
> >
> "/net/home/ymiao/.local/lib/python2.7/site-packages/ParmedTools/parmed_cmd.py",
> > line 152, in _normaldo
> > action.execute()
> > File
> >
> "/net/home/ymiao/.local/lib/python2.7/site-packages/ParmedTools/ParmedActions.py",
> > line 3772, in execute
> > parmset.read_parameter_file(pfile)
> > File
> >
> "/net/home/ymiao/.local/lib/python2.7/site-packages/chemistry/charmm/parameters.py",
> > line 525, in read_parameter_file
> > key)
> > RuntimeError: Atom type ZN not present in AtomType list
> >
>
> This occurs because one of the stream files assigns Lennard-Jones
> parameters to atom type ZN, but nowhere before that point has the ZN atom
> type ever been defined. I wasn't sure how a CHARMM parameter file parser
> was *supposed* to behave when something like this happened, so I made it a
> fatal error. This represents my general philosophy on error handling -- if
> unsure, make it a fatal error. This reduces the chances of a subtle error
> sneaking through undetected and ruining results and makes future
> adjustments easy to make if need be.
>
> If you're still getting this error even after you fix up your chamber
> command above, look for the ZN atom types in one of your parameter files
> and see if it has an analogous definition in any of your topology files (or
> higher up in the parameter file).
>
>
>
> >
> > It’s strange that I have no ZN in the system. Could you possibly help me
> > looking into the problem?
> >
>
> This error is thrown when processing the parameter files and building a
> parameter set library -- the PSF file hasn't even been parsed yet.
>
> HTH,
> Jason
>
> P.S. As an aside, o
> ne of the improvements CHARMM made to their CHARMM36 family of force fields
> was to actually put the full atom type definitions in the parameter files,
> so the RTF files are actually no
>
> longer necessary
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu May 07 2015 - 10:00:04 PDT
