[AMBER] Error with running ParmEd

From: Yinglong Miao <yinglong.miao.gmail.com>
Date: Wed, 6 May 2015 09:42:31 -0700

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>
  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
  File "/net/home/ymiao/.local/lib/python2.7/site-packages/ParmedTools/ParmedActions.py", line 3772, in execute
  File "/net/home/ymiao/.local/lib/python2.7/site-packages/chemistry/charmm/parameters.py", line 525, in read_parameter_file
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 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
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Received on Wed May 06 2015 - 10:00:02 PDT
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