Thanks for the suggestion, I'm quite lazy in changing my habits but I
guess this is a good occasion to move to NetCDF format...
Best wishes
Alessandro
Il giorno mer, 30/01/2013 alle 10.23 -0500, Jason Swails ha scritto:
> 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
> > > >
> > >
> > >
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 30 2013 - 07:30:04 PST
