Re: [AMBER] MMPBSA error

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Tue, 17 Apr 2012 14:40:58 +0200

Ugh, I've attached a new version of MMPBSA.diff.


A semi-serious side note:
For Python coders, contributing to other Python code is much more fun if
PEP8 is obeyed:
http://www.python.org/dev/peps/pep-0008

For example:
- Use 4 spaces per indentation level.
- Compound statements (multiple statements on the same line) are
generally discouraged.

Maybe something to consider in the future :)


Jan-Philip


On 04/17/2012 02:28 PM, Jan-Philip Gehrcke 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
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>



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Received on Tue Apr 17 2012 - 06:00:05 PDT
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