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:
> 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
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
It’s strange that I have no ZN in the system. Could you possibly help me looking into the problem?
Much appreciated,
Yinglong
---
Yinglong Miao, Ph.D.
Research Associate
Prof. J. Andrew McCammon Group
Howard Hughes Medical Institute
University of California, San Diego
Tel: 858-822-0255; Email: yimiao.ucsd.edu
http://mccammon.ucsd.edu/~ymiao/
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Received on Wed May 06 2015 - 10:00:02 PDT
