Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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The meaning of .grd output #267

Open wt12318 opened 1 year ago

wt12318 commented 1 year ago

Hi,

I want to get the electrostatic potential for every 3D grid point and used the APBS tools, the following is the input file:

read
  mol pqr egfr.pqr
end
elec name solv # Electrostatics calculation on the solvated state
  mg-manual # Specify the mode for APBS to run
  dime 97 97 97 # The grid dimensions
  nlev 4 # Multigrid level parameter
  grid 1 1 1 # Grid spacing
  gcent mol 1 # Center the grid on molecule 1
  mol 1 # Perform the calculation on molecule 1
  lpbe # Solve the linearized Poisson-Boltzmann equation
  bcfl sdh # Use all multipole moments when calculating the potential
  pdie 2.0 # Solute dielectric
  sdie 78.54 # Solvent dielectric
  chgm spl2 # Spline-based discretization of the delta functions
  srfm mol # Molecular surface definition
  srad 1.4 # Solvent probe radius (for molecular surface)
  swin 0.3 # Solvent surface spline window (not used here)
  sdens 10.0 # Sphere density for accessibility object
  temp 298.15 # Temperature
  calcenergy comps # Calculate energies
  calcforce no # Do not calculate forces
  write pot uhbd ./egfr.pqr
end
quit

But I don't understand the .grd output:

[wt@localhost apbs]$ head  egfr.pqr.grd
                                                        POTENTIAL (kT/e)
 1.00000e+00 0.00000e+00     -1      0     97      1     97
     97     97     97 1.00000e+00-2.53505e+01-3.43200e+01-4.15760e+01
 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
 0.00000e+00 0.00000e+00      0      0
      1     97     97
 -2.56761e-01 -2.58694e-01 -2.60648e-01 -2.62624e-01 -2.64623e-01 -2.66645e-01
 -2.68691e-01 -2.70764e-01 -2.72864e-01 -2.74992e-01 -2.77149e-01 -2.79337e-01
 -2.81557e-01 -2.83810e-01 -2.86099e-01 -2.88423e-01 -2.90785e-01 -2.93185e-01
 -2.95625e-01 -2.98105e-01 -3.00628e-01 -3.03193e-01 -3.05802e-01 -3.08455e-01

It seems have 6 columns, which columns are 3D coordinate of grid point and which column is the electrostatic potential? Thank you.