Well, by decompressing the trajectory before running mmpbsa it seems
working (the job is not finished yet, but snapshots have been generated
and the GB part is running).
It probably is an issue with zlibs or bzip2 and ccptraj (in amber11 it
worked, but ptraj was used).
Thanks again
Alessandro
Il giorno mer, 30/01/2013 alle 08.35 -0500, Jason Swails ha scritto:
> 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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Received on Wed Jan 30 2013 - 07:30:03 PST
