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
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Received on Wed May 02 2012 - 13:00:02 PDT
