Hi Jason,
here is the output when "print output" is placed after outputlines =
output.split('\n')"
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...
CPPTRAJ: Trajectory Analysis. V12.5
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
>
[trajin /archive/acontini/tubuline/md/tetramer/cp1/from_empty_equil12/csearch/tetramer_cp1_csearch.prod4.mdcrd.bz2]
Warning: /archive/acontini/tubuline/md/tetramer/cp1/from_empty_equil12/csearch/tetramer_cp1_csearch.prod4.mdcrd.bz2: Uncompressed size of trajectory could not be determined.
(This is normal for bzipped files)
Number of frames could not be calculated.
Frames will be read until EOF.
[tetramer_cp1_csearch.prod4.mdcrd.bz2] contains an unknown number of
frames.
>
INPUT TRAJECTORIES:
[tetramer_cp1_csearch.prod4.mdcrd.bz2] is an AMBER trajectory, Parm 0
(with box info), unknown #frames, start=0 offset=1
Coordinate processing will occur on an unknown number of frames.
PARAMETER FILES:
0: /archive/acontini/tubuline/md/tetramer/cp1/from_empty_equil12/csearch/tetramer_cp1_csearch.top, 254878 atoms, 77696 res, ortho. box, 75972 mol, 75920 solvent mol
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 0 actions:
BEGIN TRAJECTORY PROCESSING:
Progress: '+' = 200 frames processed.
.....................................................
PARM [tetramer_cp1_csearch.top]: Setting up 0 actions.
----- [tetramer_cp1_csearch.prod4.mdcrd.bz2] (1-EOF, 1) -----
0 +++++Error: FileIO_Bzip2::Read: BZ2_bzRead error:
[BZ_SEQUENCE_ERROR]
size=1 count=6193561
Read 1000 frames and processed 1000 frames.
ACTION OUTPUT:
DATASETS:
There are no data sets set up for analysis.
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 592, in
Query
num_frames = int(line.split()[5])
ValueError: invalid literal for int() with base 10: 'an'
Exiting. All files have been retained.
Might be an issue with bzip2? In the meanwhile I try to decompress
before running mmpbsa.py
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 - 07:00:03 PST
