APBS

Adaptive Poisson-Boltzmann Solver
Home page: http://apbs.sourceforge.net/

Version 3.4.0 is installed on Aurora (Aug 2022):
moule add GCC/10.2.0 OpenMPI/4.0.5 APBS/3.4.0

Version 3.0 installed by Ulf Nov. 2021 in /temp4/bio/APBS/APBS-3.0.0/APBS-3.0.0.Linux/bin/apbs
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/temp4/bio/APBS/APBS-3.0.0/APBS-3.0.0.Linux/lib
Downloaded from https://sourceforge.net./porojects/apbs (Files - apbs - APBS-3.0.0 - APBS-3.0.0_Linux.zip)

Version 1.5 installed by Alfonso Dec. 2016 in
/temp4/bio/APBS/APBS-1.5/bin/apbs
You need to set
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/temp4/bio/APBS/APBS-1.5/lib
to run the program; Otherwise you get
apbs: error while loading shared libraries: libmaloc.so.1: cannot open shared object file: No such file or directory

Version 1.0
Installed in /home/bio/APBS/bin/apbs

Template input file (with large grid):
# READ IN MOLECULES
read
mol pqr temp.pqr
end

elec name solv # Electrostatics calculation on the solvated state
        mg-manual # Specify the mode for APBS to run
        dime 225 225 225 # The grid dimensions
        nlev 4 # Multigrid level parameter
        grid 0.10 0.10 0.10 # 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 mdh # Use all multipole moments when calculating the potential
        pdie 1.0 # Solute dielectric
        sdie 78.39 # 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 total # Calculate energies
        calcforce no # Do not calculate forces
end

elec name ref # Calculate potential for reference (vacuum) state
        mg-manual
        dime 225 225 225
        nlev 4
        grid 0.10 0.10 0.10
        gcent mol 1
        mol 1
        lpbe
        bcfl mdh
        pdie 1.0
        sdie 1.0
        chgm spl2
        srfm mol
        srad 1.4
        swin 0.3
        sdens 10.0
        temp 298.15
        calcenergy total
        calcforce no
end

# Calculate solvation energy
print energy solv - ref end

quit

The program has been installed and tested only by Pär.