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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:
.grd
[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.
The text was updated successfully, but these errors were encountered:
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Hi,
I want to get the electrostatic potential for every 3D grid point and used the APBS tools, the following is the input file:
But I don't understand the
.grd
output:It seems have 6 columns, which columns are 3D coordinate of grid point and which column is the electrostatic potential? Thank you.
The text was updated successfully, but these errors were encountered: