Request for your help in running g_mmbpsa command.
I have given the following command for my protein (particularly NBD domain-384 residues) and an inhibitor as the ligand.
Command:g_mmpbsa -f trajfinal.xtc -s md_0_1.tpr -i pbsa.mdp -pbsa -mm energy_MM.xvg -pol polar.xvg -apol apolar.xvg -b 55000 -e 100000 -dt 10 -n index.ndx.
It has been four days already but the simulation has not stopped , It seems to be going In a loop motion even though the output files for this command have been generated. I tried troubleshooting but I'm unable to reach a conclusion. The screenshot during run is as follows:
Parsing input file p1bH3XoA.in...
Vio_ctor2: Gethostbyname fail INET sock <> dueto <ENOENT>
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
NOsh: Deprecated use of ION keyword! Use key-value pairs
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from p1bH3XoA.pqr.
Vio_ctor2: Gethostbyname fail INET sock <> dueto <ENOENT>
3808 atoms
Centered at (4.141e+01, 3.523e+01, -1.536e+01)
Net charge -4.00e+00 e
Preparing to run 4 PBE calculations.
----------------------------------------
CALCULATION #1 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 7.95385 A
Current memory usage: 506.917 MB total, 3170.576 MB high water
Grid dimensions: 129 x 129 x 129
Grid spacings: 1.181 x 1.049 x 1.758
Grid lengths: 151.196 x 134.272 x 225.003
Grid center: (62.651, 51.820, 28.170)
Multigrid levels: 6
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 80.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see
io.mc* for details)...
Calculating energy (see
io.mc* for details)...
Total electrostatic energy = 1.311467158546E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 7.95385 A
Current memory usage: 506.917 MB total, 3170.576 MB high water
Grid dimensions: 129 x 129 x 129
Grid spacings: 0.497 x 0.477 x 0.527
Grid lengths: 63.630 x 61.020 x 67.441
Grid center: (41.568, 35.073, -15.610)
Multigrid levels: 6
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 80.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see
io.mc* for details)...
Calculating energy (see
io.mc* for details)...
Total electrostatic energy = 1.387168343604E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 0.889267 A
Current memory usage: 506.917 MB total, 3170.576 MB high water
Grid dimensions: 129 x 129 x 129
Grid spacings: 1.181 x 1.049 x 1.758
Grid lengths: 151.196 x 134.272 x 225.003
Grid center: (62.651, 51.820, 28.170)
Multigrid levels: 6
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see
io.mc* for details)...
Calculating energy (see
io.mc* for details)...
Total electrostatic energy = 2.708012514367E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (1.81 A) for exclusion function
Debye length: 0.889267 A
Current memory usage: 506.917 MB total, 3170.576 MB high water
Grid dimensions: 129 x 129 x 129
Grid spacings: 0.497 x 0.477 x 0.527
Grid lengths: 63.630 x 61.020 x 67.441
Grid center: (41.568, 35.073, -15.610)
Multigrid levels: 6
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
0.950 A-radius, 1.000 e-charge, 0.150 M concentration
1.810 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Solving PDE (see
io.mc* for details)...
Calculating energy (see
io.mc* for details)...
Total electrostatic energy = 1.535080904662E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (mol1) - 2 (mol2) end
Local net energy (PE 0) = -1.479125610586E+04 kJ/mol
Global net ELEC energy = -1.479125610586E+04 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 3170.576 MB high water
Thanks for using APBS!