At line 587, can you add
print output
either after or before "outputlines = output.split('\n')
in $AMBERHOME/bin/MMPBSA_mods/make_trajs.py then re-run it again and send
me the output?
Thanks!
Jason
On Wed, Jan 30, 2013 at 7:54 AM, Alessandro Contini <
alessandro.contini.unimi.it> wrote:
> Dear Jason, thanks for your answer.
> I've rerun the job as suggested and here is the output:
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/amber12/bin/sander
> mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> File "/usr/local/amber12/bin/MMPBSA.py", line 516, in <module>
> str(external_progs['cpptraj']))
> File "/usr/local/amber12/bin/MMPBSA_mods/make_trajs.py", line 57, in
> make_trajectories
> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> File "/usr/local/amber12/bin/MMPBSA_mods/make_trajs.py", line 453, in
> __init__
> self.Query()
> File "/usr/local/amber12/bin/MMPBSA_mods/make_trajs.py", line 591, in
> Query
> num_frames = int(line.split()[5])
> ValueError: invalid literal for int() with base 10: 'an'
> Exiting. All files have been retained.
>
>
> Thanks,
>
> Alessandro
>
> Il giorno mer, 30/01/2013 alle 07.29 -0500, Jason Swails ha scritto:
>
> > On Wed, Jan 30, 2013 at 6:47 AM, Alessandro Contini <
> > alessandro.contini.unimi.it> wrote:
> >
> > > Dear community,
> > > I've recently installed amber12 (composer XE 2013.1.117) and I'm
> > > experiencing an error while running mmpbsa.py on a system where I've
> > > previously run the very same calculation with amber11.
> > >
> > > here follows the input:
> > >
> > > GB/PBSA analysis
> > > &general
> > > startframe=1, endframe=1000, interval=20, verbose=2, keep_files=0,
> > > strip_mask=:WAT,MG2,Na+,GTP,GDP,:1-438
> > > /
> > > &gb
> > > igb=2, saltcon=0.150,
> > > /
> > > &pb
> > > istrng=0.15, fillratio=4.0
> > > /
> > >
> > >
> > > I've launched mmpbsa.py trough the following command:
> > >
> > > /usr/local/amber12/bin/MMPBSA.py -O -i mmpbsa_py.in -o
> MMPBSA_PB-GB.txt
> > > -sp solvated_complex.top -cp complex.top -rp rec.top -lp lig.top -y
> > > traj.mdcrd.bz2 >& mmpbsa_py.out
> > >
> > > and this is the output:
> > >
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > ValueError: invalid literal for int() with base 10: 'an'
> > >
> >
> > This is an uncaught Python exception. I'm not sure where it's coming
> from.
> > Can you put "debug_printlevel=2" in the &general section of your input
> > file and run it again?
> >
> > Thanks,
> > Jason
> >
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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 Wed Jan 30 2013 - 06:00:06 PST
