Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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Broken example - TABI-PB (Boundary Element Method) #213

Open tomer196 opened 2 years ago

tomer196 commented 2 years ago

I was trying to run the example of the TABI-PB (Boundary Element Method) - link.
Running the following command: apbs 1a63_NanoShaper_SES.in gave the following error:
image

I didn't change the input file:

read
    mol pqr test_proteins/1a63.pqr       # PQR location 
end
elec name comp_solv        # Solvated complex
    tabi

    mol 1
    ion charge 1           # sodium ions
        conc 0.15 
        radius 0.95
    ion charge -1          # chloride ions
        conc 0.15 
        radius 1.81       
    pdie 1.0               # Solute dielectric
    sdie 80.00             # Solvent dielectric
    srad 1.4               # Solvent probe radius
    sdens 1                # NO. of Elements per A^2
    temp 300.00            # Temperature

    tree_order 3           # taylor expansion order
    tree_n0 500            # maxium particle per leaf
    mac 0.8                # multipole acceptance criterion

    mesh ses               # mesh options: ses, skin. Options ses and skin require nonoshaper.

    outdata 1              # outdata (0 - dat file, 1 - dat and VTK file)
end

quit

Anyone knows how to fix it?

intendo commented 2 years ago

Can you tell us what operating system and version you are using? What version of APBS are you using?

I can't reproduce the problem in Ubuntu 20.

Did you build APBS from src or are you using the newest binary of APBS?