Forgot to mention
In any "entropy outputs" I've not detected any errors besides warnings in
the
_MMPBSA_cpptraj_entropy.out
ACTION OUTPUT:
Warning: In covariance matrix 'comp.matrix', # of frames 100 is less than
Warning: # of columns 14160. If diagonalized, the max # of non-zero
Warning: eigenvalues will be 100
Warning: In covariance matrix 'rec.matrix', # of frames 100 is less than
Warning: # of columns 13998. If diagonalized, the max # of non-zero
Warning: eigenvalues will be 100
Warning: In covariance matrix 'lig.matrix', # of frames 100 is less than
Warning: # of columns 162. If diagonalized, the max # of non-zero
Warning: eigenvalues will be 100
or many many warnings like
warning: setting vibrational entropy to zero for mode 9413 with vtemp =
-14945443.762680
warning: setting vibrational entropy to zero for mode 9414 with vtemp =
-14939332.231481
warning: setting vibrational entropy to zero for mode 9415 with vtemp =
-14933726.365450
warning: setting vibrational entropy to zero for mode 9416 with vtemp =
-14926595.749537
warning: setting vibrational entropy to zero for mode 9417 with vtemp =
-14922297.649364
warning: setting vibrational entropy to zero for mode 9418 with vtemp =
-14915258.643458
James
2014-04-28 10:58 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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...
>
> Beginning quasi-harmonic calculations with
> /home/own/Documents/simulations/amber/amber14/bin/cpptraj
>
> Beginning quasi-harmonic calculations with
> /home/own/Documents/simulations/amber/amber14/bin/cpptraj
>
> Beginning quasi-harmonic calculations with
> /home/own/Documents/simulations/amber/amber14/bin/cpptraj
>
> Beginning quasi-harmonic calculations with
> /home/own/Documents/simulations/amber/amber14/bin/cpptraj
> 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.
>
> 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 ?
> 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. How such solute's
> vibrational entropy could contribute to the total dG?
>
> James
>
>
> 2014-04-26 18:24 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
> On Sat, Apr 26, 2014 at 10:12 AM, James Starlight <jmsstarlight.gmail.com
>> >wrote:
>>
>> > Jason,
>> >
>> > works perfect.
>> > Using igb=2, saltcon=0.150,
>> > I've obtained below results for the high affinity agonist of my membrane
>> > receptor (here protein's entropy had not been taken into account):
>> >
>> > Differences (Complex - Receptor - Ligand):
>> > Energy Component Average Std. Dev. Std. Err.
>> of
>> > Mean
>> >
>> >
>> -------------------------------------------------------------------------------
>> > VDWAALS -49.2645 3.5945
>> > 0.3595
>> > EEL -139.6615 6.8852
>> > 0.6885
>> > EGB 136.3443 5.7616
>> > 0.5762
>> > ESURF -7.5376 0.1172
>> > 0.0117
>> >
>> > DELTA G gas -188.9260 7.1462
>> > 0.7146
>> > DELTA G solv 128.8067 5.7253
>> > 0.5725
>> >
>> > DELTA TOTAL -60.1193 3.6655
>> > 0.3665
>> >
>> > It's looks very good. But why EEL and EGB are so differs in sights?
>> >
>>
>> That is the nature of those potential terms -- they are competing
>> effects.
>> I would suggest familiarizing yourself with the theory of solvation and
>> the GB equations if you want deeper insight as such compensatory behavior
>> is very common. Also, if you look at the thermodynamic cycle and analyze
>> what is happening on the microscopic scale for each step it should make
>> sense. (Think about what the solvent molecules are doing and how each
>> component of the system interacts with each other and how those
>> interactions change along each step of the reaction coordinate).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Apr 28 2014 - 00:30:03 PDT
