D'oh!
No I didn't - but I did now, and then I get an error about a wrong PSF molecule section:
> chamber -top top_all36_lipid.rtf -top top_all36_cgenff.rtf -param par_all36_lipid.prm -param par_all36_cgenff.prm -str toppar_all36_lipid_cholesterol.str -str toppar_water_ions.str -psf step5_assembly.psf -crd step5_assembly.pdb -box 72.5,72.5,82 -nocmap
Creating chamber topology file from PSF step5_assembly.psf, RTF files [top_all36_lipid.rtf, top_all36_cgenff.rtf], PAR files [par_all36_lipid.prm, par_all36_cgenff.prm], and STR files [toppar_all36_lipid_cholesterol.str, toppar_water_ions.str]. Coords from step5_assembly.pdb. NO CMAP. Box info [72.5, 72.5, 82.0, 90.0, 90.0, 90.0]. GB Radius set mbondi.
CharmmPSFWarning: Detected PSF molecule section that is WRONG. Resetting molecularity.
AmberParmWarning: POINTERS flag not found! Likely a bad AMBER topology file.
Traceback (most recent call last):
File "ParmEd/parmed.py", line 161, in <module>
parmed_commands.cmdloop()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py", line 219, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File "/Users/witzke/ParmEd/ParmEd/ParmedTools/parmed_cmd.py", line 141, in _normaldo
action.execute()
File "/Users/witzke/ParmEd/ParmEd/ParmedTools/ParmedActions.py", line 3563, in execute
parm.load_coordinates(coords)
File "/Users/witzke/ParmEd/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'
Could I have cloned the repository wrong (since I am not so familiar with this)?
Best regards,
Sarah
Den 14/08/2014 kl. 18.48 skrev Jason Swails <jason.swails.gmail.com>:
> On Thu, Aug 14, 2014 at 12:31 PM, Sarah Witzke <witzke.sdu.dk> wrote:
>
>> Hi Jason,
>>
>> I have downloaded the latest ParmEd from your github (just a couple of
>> hours ago) and done "python setup.py build", "python setup.py install".
>> When I run ParmEd I give the full path to this executable to make sure I
>> use this version.
>> I have a pdb and a psf file of a membrane containing POPC and ergosterol
>> from the charmm-membrane-builder-gui. When I try to use chamber in ParmEd
>> with this command:
>> *****
>> chamber -top top_all36_lipid.rtf -top top_all36_cgenff.rtf -param
>> par_all36_lipid.prm -param par_all36_cgenff.prm -str
>> toppar_all36_lipid_cholesterol.str -str toppar_water_ions.str -psf
>> step5_assembly.psf -crd step5_assembly.pdb -box 72.5,72.5,82 -nocmap
>> *****
>> I get this error:
>> *****
>> Creating chamber topology file from PSF step5_assembly.psf, RTF files
>> [top_all36_lipid.rtf, top_all36_cgenff.rtf], PAR files
>> [par_all36_lipid.prm, par_all36_cgenff.prm], and STR files
>> [toppar_all36_lipid_cholesterol.str, toppar_water_ions.str]. Coords from
>> step5_assembly.pdb. NO CMAP. Box info [72.5, 72.5, 82.0, 90.0, 90.0, 90.0].
>> GB Radius set mbondi.
>> Traceback (most recent call last):
>> File "/Users/witzke/ParmEd-1.1/parmed.py", line 161, in <module>
>> parmed_commands.cmdloop()
>> File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
>> line 142, in cmdloop
>> stop = self.onecmd(line)
>> File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
>> line 219, in onecmd
>> return func(arg)
>> File "<string>", line 1, in <lambda>
>> File "/Users/witzke/ParmEd-1.1/ParmedTools/parmed_cmd.py", line 141, in
>> _normaldo
>> action.execute()
>> File "/Users/witzke/ParmEd-1.1/ParmedTools/ParmedActions.py", line 3563,
>> in execute
>> parm.load_coordinates(coords)
>> File "/Users/witzke/ParmEd-1.1/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'
>> *****
>>
>> It seems similar to en error Marc had previously but I can't figure out
>> what I should do differently. Do you have an idea?
>>
>
> Did you clone the repository or download one of the releases? You need to
> clone the repo to get a working chamber action. I'm in the middle of
> something that is preventing me from issuing another release (hopefully
> done in a week or so).
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Aug 14 2014 - 10:30:02 PDT
