Hi Jason,
I tried with 'debug_printlevel=2' and now it is giving this error:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using mmpbsa_py_energy
cpptraj found! Using cpptraj
Preparing trajectories for simulation...
File "/usr/local/AmberTools/bin/MMPBSA.py", line 516, in <module>
str(external_progs['cpptraj']))
File "/usr/local/AmberTools/bin/MMPBSA_mods/make_trajs.py", line 57, in make_trajectories
traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
File "/usr/local/AmberTools/bin/MMPBSA_mods/make_trajs.py", line 453, in __init__
self.Query()
File "/usr/local/AmberTools/bin/MMPBSA_mods/make_trajs.py", line 577, in Query
process = Popen([self.exe, self.prmtop], stdin=PIPE, stdout=PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1092, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Exiting. All files have been retained.
Thanks,
Sonu
On Apr 12, 2012, at 2:56 PM, Jason Swails wrote:
> Can you add "debug_printlevel=2" to the &general section of your MMPBSA
> input file and retry it? That will provide a full traceback so I can see
> where the error is really occurring.
>
> Thanks!
> Jason
>
> On Wed, Apr 11, 2012 at 5:24 PM, Kumar, Sonu
> <sonu.kumar.dkfz-heidelberg.de>wrote:
>
>> Hi All,
>>
>> I am using MMPBSA.py module of AmberTool12 which is on my institute
>> cluster for energy calculation, but getting an error?
>>
>> Here is my input file:
>> mmpbsa.in
>> Input file for running PB and GB in serial
>> &general
>> endframe=50, keep_files=2,
>> /
>> &gb
>> igb=2, saltcon=0.100,
>> /
>> &pb
>> istrng=0.100,
>> /
>>
>> /usr/local/AmberTools/bin/MMPBSA.py -O -i mmpbsa.in -o
>> FINAL_RESULTS_MMPBSA.dat -sp complex_solvated.prmtop -cp complex.prmtop -rp
>> rec.prmtop -lp lig.prmtop -y *.crdbox
>>
>> Error which I am getting after running above command:
>>
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> mmpbsa_py_energy found! Using mmpbsa_py_energy
>> cpptraj found! Using cpptraj
>> Preparing trajectories for simulation...
>> OSError: [Errno 2] No such file or directory
>> Exiting. All files have been retained.
>>
>>
>> It would be great if someone help me in this..
>>
>> Thanks
>> Sonu
>>
>> ----------------
>> Sonu Kumar, M.Sc
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
----------------
Sonu Kumar, M.Sc
GlycoImmunology Lab(D015)
German Cancer Research Center(DKFZ),
Heidelberg, Germany
sonu.kumar.dkfz.de
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Received on Tue Apr 17 2012 - 04:00:03 PDT
