Thanks Jason.
Now it is working. It was path setting prob.
Thanks
Sonu
On Apr 17, 2012, at 4:07 PM, Jason Swails wrote:
> A nice detailed analysis! This is exactly what's happening. I'm confused
> why this particular issue exists, since I distinctly remember addressing
> this, but I must not have committed it :(. While this patch works, I'm a
> little concerned about what may happen in parallel. To avoid having to
> know when each thread knows about everything, I typically quit after a
> fatal error by throwing an uncaught exception (I modified the excepthook to
> optionally suppress the traceback and call MPI.Abort to kill all threads).
> I'll create a patch for this.
>
> Back to the OP, though -- all this patch will do is provide a more helpful
> error message -- the problem is that cpptraj is not installed, and it needs
> to be for MMPBSA.py to work. Make sure you install all of AmberTools 12,
> and that each of the mmpbsa_py tests pass, before trying to perform your
> own simulations.
>
> As a side note, if cpptraj _is_ installed, make sure AMBERHOME is properly
> set (to your AmberTools installation, NOT your older Amber installation --
> see http://jswails.wikidot.com/installing-ambertools-12-and-older-amber for
> details).
>
> HTH,
> Jason
>
> On Tue, Apr 17, 2012 at 8:28 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
>> wrote:
>
>> Huhu,
>>
>> "OSError: [Errno 2] No such file or directory" in context of subprocess
>> means that the executable path provided to `subprocess.Popen()` is not a
>> valid path. This is contradictory to the message "cpptraj found! Using
>> cpptraj". Likewise, there must be a problem in the source code.
>>
>> I went through AmberTools12's MMPBSA source, and if I am not overseeing
>> something elementary, I found this problem. However, I did not compile
>> AmberTools12 myself so far and did not run any tests. So in case I've
>> overseen something, I may have identified the problem wrongly which also
>> renders the proposed solution to nonsense :-)
>>
>>
>> Let's look at line 37 of findprogs.py (in function `find_progs()`):
>>
>> print '%s found! Using %s' % (prog, str(my_progs[prog]))
>>
>> which in Kumar's case resulted in "cpptraj found! Using cpptraj".
>>
>>
>> From the code in context, `prog` is the 'required' program name, in this
>> case "cpptraj". "cpptraj found" actually means cpptraj is
>> required/requested. It does not mean that the executable has been found so
>> far.
>>
>> `str(my_progs[prog])` prints what the `__str__` method of class
>> `ExternProg` returns:
>>
>>
>> def __str__(self):
>> if self.full_path: return self.full_path
>> else: return self.prog_name
>>
>> `self.full_path` is what `which(self.prog_name, self.search_path)`
>> returns. This function returns `None` if the requested executable was
>> neither found in a) $AMBERHOME/bin nor in $PATH. Hence, if the program is
>> not found by `which()`, `self.full_path` is `None` and `self.prog_name` is
>> printed. Which does not make sense.
>>
>> This means that "cpptraj found! Using cpptraj" is printed even if the
>> cpptraj executable is not found. The same is true for any other required
>> program.
>>
>> A `None` returned by `which()` indicates that the executable was not
>> found. However, I cannot find any place where a `None` returned by
>> `which()` results in an error message. I think that `find_progs()` should
>> return `False` or `None` in case one of the requested executables could not
>> be found. Then, in MMPBSA.py(cc), after line 497:
>>
>> external_progs = find_progs(INPUT)
>>
>> we should check for `external_progs` being `None` or `False`. I attached
>> two patch files implementing these suggestions. Again, I did not test
>> anything of this.
>>
>> This is only a suggestion and maybe it helps,
>>
>> Jan-Philip
>>
>>
>>
>>
>>
>>
>> On 04/17/2012 12:51 PM, Kumar, Sonu wrote:
>>
>>> 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<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<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
>>>
>>>
>>> ______________________________**_________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>
>>
>> _______________________________________________
>> 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 - 07:30:04 PDT
