Segmentation Fault when using Pymol and APBS

APBS is a software package for modelling biomolecule solvation. Which means, it is useful for getting to know the electrostatics of your protein at a given pH. You can learn more about it here: It can be neatly integrated with Pymol to give a visual representation of such electrostatics. But, if you install it in Ubuntu (try apt-getting apbs) it will likely crash with a wonderful “Segmentation Fault” message.

SOLUTION: Uninstall Tcl8.4 and Tk8.4. You’ll likely have 8.5 version installed and it will conflict and cause the seg fault.

Another thing I came across, when using PDB2PDQ servers to generate the *pqr and *in files, your protein MIGHT have some problems. Look at this:

ATOM      1  N   SER     1     -25.705  -7.533-149.407  0.1849 1.8240
ATOM      2  CA  SER     1     -26.409  -7.267-148.130  0.0567 1.9080
ATOM      3  CB  SER     1     -27.933  -7.360-148.311  0.2596 1.9080

It might seem normal for a PDB file, where every field is LENGTH delimited. However, PQR files are WHITESPACE delimited (which makes much more sense actually) and the y/z coordinates are actually non-separated because of the big value and the negative sign! So, it crashes when opening APBS due to a parsing error.

SOLUTION: Make sure that there is no such thing as glued fields (usually negative XYZ coordinates). If you’re using linux try this: sed -i ‘s/\([0-9]\)\(\-\)/\1 \2/’ your_protein.pqr

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