Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids

From: <anilkumarsahoo.physics.iisc.ernet.in>
Date: Wed, 26 Aug 2015 05:34:47 +0530

Hi Dan,

I checked the trajectory through the cpptraj 'check' command and found no
issue. I tried to run with the serial version also, it is giving the same
error as printed bellow.

 File "/home/anilkumarsahoo/amber14/bin/MMPBSA.py", line 104, in ?
    app.parse_output_files()
  File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/main.py", line 928,
in parse_output_files
    self.using_chamber)}
  File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 634, in __init__
    AmberOutput._read(self)
  File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 343, in _read
    self._get_energies(output_file)
  File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 661, in _get_energies
    self.data['VDWAALS'].append(float(words[2]))
ValueError: invalid literal for float(): *************
Exiting. All files have been retained.

Any help will be really appreciated.

Thanks
Anil



> Seems like your coordinates may have some issues. Try running the
> trajectory through the cpptraj 'check' command to see if you have bad
> overlaps. Also, you may want to try running a few frames in serial to
> see if you have similar problems.
>
> -Dan
>
> On Tue, Aug 25, 2015 at 5:29 AM, <anilkumarsahoo.physics.iisc.ernet.in>
> wrote:
>> Dear AMBER users,
>>
>> I have installed MMPBSA.py.MPI module of AmberTools14 and am able to
>> perform binding energy calculation using that. But when I am including
>> any
>> Lipid residue in the system, it is giving the following error
>>
>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA.py.MPI", line 104, in ?
>> app.parse_output_files()
>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/main.py", line 928,
>> in parse_output_files
>> self.using_chamber)}
>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>> line 634, in __init__
>> AmberOutput._read(self)
>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>> line 343, in _read
>> self._get_energies(output_file)
>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>> line 661, in _get_energies
>> self.data['VDWAALS'].append(float(words[2]))
>> ValueError: invalid literal for float(): *************
>> Error occured on rank 0.
>> Exiting. All files have been retained.
>>
>>
>> My input file for the calculation is given bellow.
>>
>> &general
>> startframe=1, endframe=200, interval=1, keep_files=2, verbose=2,
>> netcdf=1, use_sander=1,
>> /
>> &gb
>> igb=2, saltcon=0.0,
>> /
>>
>> Thanks for any help,
>> Anil Kumar Sahoo
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> 



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 25 2015 - 18:00:03 PDT
Custom Search