On Mon, Apr 30, 2012 at 5:25 PM, manikanthan bhavaraju <mhb75.msstate.edu>wrote:
> Dear All,
> I am trying to calculate per-residue decomposition analysis using
> ambertools1.5 for protein-ligand system. I am following the exact
> instruction given in the amber tutorial 3 -section 3.6
> Here is the input file
> Per-residue GB and decompositon
> &general
> endframe=50, keep_files=2,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &decomp
> idecomp=2, dec_verbose=3,
>
You are missing a "/" here to terminate the &decomp namelist, so it doesn't
understand that you want decomposition analysis.
I would also suggest upgrading to AmberTools 12, which has an updated
version of MMPBSA.py. I think the input file parser was improved, and
would probably catch errors like this.
> And I am getting 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/amber11/bin/mmpbsa_py_energy
> cpptraj found! Using /home/srg/mhb75/Download/amber11/bin/cpptraj
> Preparing trajectories for simulation...
> ValueError: invalid literal for int(): EOF
>
I'm not sure what error you hit here. However, based on your input file,
MMPBSA.py shouldn't ever look for mmpbsa_py_energy, so maybe fixing your
input file will solve this problem.
Exiting. All files have been retained.
>
> I didn't understood the error message "ValueError: invalid literal for
> int()". To which value is it referring to?
>
This is actually a Python exception. These types of errors usually print
out a traceback that shows exactly where this error occurred, but for some
reason it's not printed in your output (it's suppressed by default in
AmberTools 12, but it should always be printed for AmberTools 1.5).
Without the traceback, it will be difficult for me to find out where
things are going wrong.
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 30 2012 - 15:30:03 PDT
