Re: [AMBER] error in decomposition analysis using ambertools 1.5

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 May 2012 11:41:05 -0400

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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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 01 2012 - 09:00:03 PDT
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