Re: [AMBER] Error with running ParmEd

From: Jason Swails <>
Date: Wed, 6 May 2015 21:59:27 -0400

On Wed, May 6, 2015 at 12:42 PM, Yinglong Miao <>

> Dear All,
> I have been trying to convert vmd-generated psf/pdb files for a
> membrane-protein system using newly installed from
> 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 (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/", line 183, in <module>
> parmed_commands.cmdloop()
> File "/usr/lib/python2.7/", line 142, in cmdloop
> stop = self.onecmd(line)
> File "/usr/lib/python2.7/", line 221, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File
> "/net/home/ymiao/.local/lib/python2.7/site-packages/ParmedTools/",
> line 152, in _normaldo
> action.execute()
> File
> "/net/home/ymiao/.local/lib/python2.7/site-packages/ParmedTools/",
> line 3772, in execute
> parmset.read_parameter_file(pfile)
> File
> "/net/home/ymiao/.local/lib/python2.7/site-packages/chemistry/charmm/",
> 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.


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
Rutgers University
Postdoctoral Researcher
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Received on Wed May 06 2015 - 19:00:03 PDT
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