Hi Jason,
I am also getting same error as Mani got. As you said to try search_path=1 but it didn't work.
Here is my error:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using sander
mmpbsa_py_energy found! Using /usr/local/AmberTools/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/AmberTools/bin/cpptraj
Preparing trajectories for simulation...
1000 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with None
File "/usr/local/AmberTools/bin/MMPBSA.py", line 565, in <module>
external_progs, '_MMPBSA_', normal_system)
File "/usr/local/AmberTools/bin/MMPBSA_mods/calculation.py", line 91, in run_calculations
if 'mmpbsa_py_energy' in progs['gb']: incrd = '%scomplex.pdb' % prefix
TypeError: argument of type 'NoneType' is not iterable
Exiting. All files have been retained.
Thanks
Sonu
On May 1, 2012, at 5:41 PM, Jason Swails wrote:
> You need Amber (sander) to do decomp analysis. If you want to do decomp
> with AmberTools 12 but use sander from Amber 11, you need to put
> "search_path=1" in the &general section of your input file.
>
> Can you try this?
>
> On Mon, Apr 30, 2012 at 9:13 PM, manikanthan bhavaraju <
> manikanthanbhavaraju.gmail.com> wrote:
>
>> Jason,
>>
>> I have added the debug_printlevel=2 to the general section. It is
>> showing the following error:
>>
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> sander found! Using sander
>> mmpbsa_py_energy found! Using
>> /home/srg/mhb75/Download/amber12/bin/mmpbsa_py_energy
>> cpptraj found! Using /home/srg/mhb75/Download/amber12/bin/cpptraj
>> Preparing trajectories for simulation...
>> 50 frames were processed by cpptraj for use in calculation.
>>
>> Beginning GB calculations with None
>> File "/home/srg/mhb75/Download/amber12/bin/MMPBSA.py", line 565, in ?
>> external_progs, '_MMPBSA_', normal_system)
>> File "/home/srg/mhb75/Download/amber12/bin/MMPBSA_mods/calculation.py",
>> line 91, in run_calculations
>> if 'mmpbsa_py_energy' in progs['gb']: incrd = '%scomplex.pdb' % prefix
>> TypeError: iterable argument required
>>
> Exiting. All files have been retained.
>>
>> Is the python 2.4 version on my computer having issues with amber12tools?
>>
>> mani
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
----------------
Sonu Kumar, M.Sc
GlycoImmunology Lab(D015)
German Cancer Research Center(DKFZ),
Heidelberg, Germany
sonu.kumar.dkfz.de
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Received on Wed May 02 2012 - 04:00:04 PDT
