Decomposition analysis will not work with Amber 8. You need at least
Amber11 to use decomposition with MMPBSA.py. I will look into improving
the error messages.
The only parts that you *cannot* use without Amber 11 or Amber 12 are:
QM/MMGBSA, use_sander=1, sander_apbs=1, igb=7 or 8, and decomposition. The
remaining options are all available just through AmberTools 12.
Thanks!
Jason
On Wed, May 2, 2012 at 5:13 PM, Kumar, Sonu
<sonu.kumar.dkfz-heidelberg.de>wrote:
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
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AMBER.ambermd.org
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Received on Wed May 02 2012 - 17:00:04 PDT
