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
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> AMBER.ambermd.org
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>
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Received on Mon Apr 28 2014 - 00:30:02 PDT
