Hi Jason,
Here is my input file
> &general
> endframe=100, keep_files=2,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &decomp
> idecomp=2, dec_verbose=3,
/
I have installed only Ambertools 12 but on cluster there is Amber8 also but on different path.
Thanks
Sonu
On May 2, 2012, at 9:57 PM, Jason Swails wrote:
> What is your input file? Also, what do you have installed? AmberTools 12?
> AmberTools only (and no Amber 12?) AmberTools 12 and Amber 11?
>
> The issue I think is that you don't have the necessary programs to run the
> types of calculations you want, but the error message has to be improved.
>
> Thanks!
> Jason
>
> On Wed, May 2, 2012 at 6:46 AM, Kumar, Sonu
> <sonu.kumar.dkfz-heidelberg.de>wrote:
>
>> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 02 2012 - 14:30:03 PDT
