Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 12 Aug 2014 07:52:09 -0400

On Tue, Aug 12, 2014 at 1:50 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:

> Thanks Jason - No problem for the testing, it's in my benefit too! (a
> workflow with just needing one pass through ParmEd is preferable!).
> Anyway, I got the following error now:
>
> > chamber -top top_all36_prot_ksi.rtf -param par_all36_prot_cgenff_ksi.prm
> -psf dry.rs1_charmm.psf -crd dry.rs1.pdb
> Creating chamber topology file from PSF dry.rs1_charmm.psf, RTF files
> [top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
> Coords from dry.rs1.pdb. Using CMAP. GB Radius set mbondi.
> Traceback (most recent call last):
> File "/Users/marcvanderkamp/Documents/work/ParmEd/parmed.py", line 161,
> in <module>
> parmed_commands.cmdloop()
> File
>
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 142, in cmdloop
> stop = self.onecmd(line)
> File
>
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
> line 221, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/parmed_cmd.py",
> line 141, in _normaldo
> action.execute()
> File
> "/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/ParmedActions.py",
> line 3563, in execute
> parm.load_coordinates(coords)
> File
>
> "/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/_amberparm.py",
> line 940, in load_coordinates
> for i, atom in enumerate(self.atom_list):
> AttributeError: 'ChamberParm' object has no attribute 'atom_list'
>

​I'm at a complete loss here. It works fine for me and I can't possibly
see how you are getting these errors (and I'm not).

One thing that's a little concerning is that you've installed ParmEd, yet
the modules that it is using still seem to come from your source code
folder and not from
/home/marcvanderkamp/Library/Python/2.7/lib/python/site-packages...

Also, I'm not sure that I have the exact files you're using. I'm still
using the files from test_cgenff.tgz that you attached to an earlier
message. If I use the files as-is, I get this error:

​​
  File
"/Users/swails/Library/Python/2.7/lib/python/site-packages/ParmedTools/ParmedActions.py",
line 3561, in execute

​​
    parm = ConvertFromPSF(psf, frcfield).view(ChamberParm)

​​
  File
"/Users/swails/Library/Python/2.7/lib/python/site-packages/chemistry/amber/_chamberparm.py",
line 691, in
​​
ConvertFromPSF

​​
    rij = lj_radii[i] + lj_radii[j]
​TypeError: unsupported operand type(s) for +: 'NoneType' and 'NoneType'

which is a result of the parameter file being malformed. If I fix the prm
file (by putting the NBFIX section at the end), I get the following:

Creating chamber topology file from PSF dry.rs1_charmm.psf, RTF files
[top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
Coords from dry.rs1.pdb. Using CMAP. GB Radius set mbondi.
​Outputting Amber topology file test.parm7 and restart test.rst7
​Done!

which indicates everything worked (I've attached the test.parm7 and
test.rst7 files here). But until I can reproduce the errors you're seeing,
I don't know how I can fix it...

Thanks,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher




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Received on Tue Aug 12 2014 - 05:00:02 PDT
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