... and new error during PB calculations of my test system using:
&general
endframe=100, keep_files=2, strip_mask=':WAT,CLA,POT,POPE,POPC'
&pb
istrng=0.150, inp=1, radiopt=0
Beginning PB calculations with
/home/own/Documents/simulations/amber/amber14/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating ligand contribution...
calculating ligand contribution...
calculating ligand contribution...
calculating ligand contribution...
File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py", line
104, in <module>
app.parse_output_files()
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
line 928, in parse_output_files
self.using_chamber)}
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 708, in __init__
AmberOutput._read(self)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 343, in _read
self._get_energies(output_file)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 744, in _get_energies
self.data['ENPOLAR'].append(float(words[2]))
ValueError: could not convert string to float: minimization
Exiting. All files have been retained.
File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py", line
104, in <module>
app.parse_output_files()
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
line 928, in parse_output_files
self.using_chamber)}
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 708, in __init__
AmberOutput._read(self)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 343, in _read
self._get_energies(output_file)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 744, in _get_energies
self.data['ENPOLAR'].append(float(words[2]))
ValueError: could not convert string to float: minimization
Exiting. All files have been retained.
File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py", line
104, in <module>
app.parse_output_files()
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
line 928, in parse_output_files
self.using_chamber)}
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 708, in __init__
AmberOutput._read(self)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 343, in _read
self._get_energies(output_file)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 744, in _get_energies
self.data['ENPOLAR'].append(float(words[2]))
ValueError: could not convert string to float: minimization
Exiting. All files have been retained.
File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py", line
104, in <module>
app.parse_output_files()
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
line 928, in parse_output_files
self.using_chamber)}
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 708, in __init__
AmberOutput._read(self)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 343, in _read
self._get_energies(output_file)
File
"/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/amber_outputs.py",
line 744, in _get_energies
self.data['ENPOLAR'].append(float(words[2]))
ValueError: could not convert string to float: minimization
Exiting. All files have been retained.
I've not observed any errors in *.mdout.0 files besides some warnings in
_MMPBSA_normal_traj_cpptraj.out
19: [rmsd !(:WAT,CLA,POT,POPE,POPC) mass first]
Mask [!(:WAT,CLA,POT,POPE,POPC)] corresponds to 4720 atoms.
Mask [!(:WAT,CLA,POT,POPE,POPC)] corresponds to 4720 atoms.
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
----- test_md.dcd (1-100, 1) -----
James
2014-04-29 10:20 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Jason, David,
>
> Thanks for suggestions!
> Regarding parallel calculations: I made previous tasks exactly using
> mpirun -np 4 MMPBSA.py -i ...
> which result in those 4* outputs like
>
> Loading and checking parameter files for compatibility...
> Loading and checking parameter files for compatibility...
> Loading and checking parameter files for compatibility...
> Loading and checking parameter files for compatibility...
> ...
>
> James
>
>
> 2014-04-28 15:54 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
> On Mon, 2014-04-28 at 10:58 +0400, James Starlight wrote:
>> > Jason,
>> >
>> >
>> > many thanks for explanations again! Some error have been occurred
>> > during PB with the inclusion of entropy calculations- according to the
>> > below log It seems that problems have been associated with the
>> > quasi-harmonic analysis (This run have been initiated on 4 cores).
>> >
>> >
>> > Beginning PB calculations
>> > with /home/own/Documents/simulations/amber/amber14/bin/sander
>> > calculating complex contribution...
>> > calculating receptor contribution...
>> > calculating receptor contribution...
>> > calculating receptor contribution...
>> > calculating receptor contribution...
>> > calculating ligand contribution...
>> > calculating ligand contribution...
>> > calculating ligand contribution...
>> > calculating ligand contribution...
>>
>> It looks like you ran in parallel incorrectly. You must use the
>> MMPBSA.py.MPI executable instead of MMPBSA.py if you want to run in
>> parallel. This looks like you did
>>
>> mpirun -np 4 MMPBSA.py -i ...
>>
>> In this case you are running 4 copies of the same simulation over all
>> cores, each of which is simulating all frames and overwriting the output
>> files of each other.
>>
>> > Does it possible to make some corrections in the input data and
>> > re-start calculations from the unfinished step not performing long PB
>> > calculations from the beginning ?
>>
>> No.
>> >
>> > By the way from the general assumption the main entropy contribution
>> > to the total binding entropy should be associated with the solvent
>> > entropy which has been implicitly included in the SASA term.
>>
>>
>> The solvent entropy has been implicitly included in the entire GB
>> equation, not just the SASA term. The GB equation gives a free energy
>> -- backing the entropy contribution out of the expression is non-trivial
>> (or at least non-trivial to me).
>>
>> > How such solute's vibrational entropy could contribute to the total
>> > dG?
>>
>> If this answer was known there would be no point in computing it -- you
>> could just add it as a post-hoc correction.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>
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Received on Tue Apr 29 2014 - 23:30:02 PDT
