I was interested in your APBS electrostatics software (APBS) with Michael
> Lerner's PyMOL front-end and the vacuum electrostatics (V) generated by
> PyMOL's GUI menu, to visualize solvated and unsolvated continuum
> electrostatics respectively. The results from these two approaches exhibit
> a few differences I was hoping you could clarify:
> 1. If continuum electrostatics are of interest, are both (APBS) and (V)
> performing them? Or is the latter performing some pair-wise Coulombic
APBS is solving the Poisson-Boltzmann equation (continuum solvent
electrostatics) and the vacuum electrostatics is simply an evaluation of
Coulomb's law as you suggest.
2. The (APBS) molecular surface can be colored by low, middle, and high
> values of kT/e, and by default they are -1, 0, 1 respectively. However, the
> (V) molecular surface is automatically scaled to some negative and equal in
> magnitude positive values. Should I set these (V) values for the (APBS)
> values in order to compare these two methods with and without solvation?
I'm not sure why you would want to compare the two but, yes, you should
probably use the same potential ranges for each. Note that +/- 1 kT/e is
generally too small of a range to be useful and you might want to try +/- 5
kT/e or larger.
> 3. The PDB2PQR can handle nucleic acids and so the (APBS) molecular surface
> covers these nucleic acids. But, the (V) molecular surface does not cover
> these nucleic acids. So should any nucleic acid atom lines be deleted from
> the .pqr file before performing (APBS) so the results are equivalent to (V)?
I don't know; I'm not that familiar with the vacuum functionality in PyMOL.
I have also tried first deleting the nucleic acid atom lines in the .pdb
> file and then making a .pqr file, but then (APBS) errors with
> ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does
> 'pymol-generated.dx' exist? and the PyMOL Console indicating that
> Valist_readPQR: Error parsing atom 9! Does this mean that PDB2PQR did not
> properly make a .pqr file so that the pymol-generated.dx file could not be
I would recommend using PDB2PQR to generate all of your PQR files from PDB
files before using them with PyMOL/APBS. If the problem persists, please
check the directory settings for APBS, PyMOL, and your current working
directory. Let us know if any of these directory names have spaces in them.
> 4. Is the (ABPS) molecular surface showing only the self-charges of the
> protein (even if there are nucleic acids nearby), or is it showing the
> charges of the protein attenuated by the presence of the charges from the
> nucleic acid?
If both protein and nucleic acid atoms/charges were included in the
calculation, then the electrostatic potential from both the protein and
nucleic acid is shown on the molecular surface. Note that I generally
prefer visualizing the potential from the solvent-accessible surface on the
surface of the molecules.
> Or restated, is there a way to demonstrate charge complementarity by
> painting the charges of the nucleic acid onto the molecular surface of the
I would recommend looking at the isolated protein and nucleic acid and then
at the complex.
> Thank you,
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis