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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Received on Wed Jan 30 2013 - 05:00:04 PST
