Ah. It appears that bzip2 trajectories won't work... I'll work on getting
this fixed for the next version of MMPBSA.py, since it will be somewhat
difficult for AmberTools 12. For the time being, use either
gzip-compressed, ASCII or (best choice:) NetCDF trajectories.
Thanks!
Jason
On Wed, Jan 30, 2013 at 10:18 AM, Alessandro Contini <
alessandro.contini.unimi.it> wrote:
> 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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>
--
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 - 07:30:03 PST
