trying to use apbs with pymol, confused

[ghost]

I'm on a mac, 14.1.1, and I'm trying to find the charges of a receptor's binding site. I'm new to pymol and am not too sure about how to use apbs to visualize it in pymol (following the instructions here: https://apbs.readthedocs.io/en/latest/using/examples/visualization-pymol.html#run-the-apbs-calculation didn't work because I don't have the file location saved in my pymol). Ideally, I'd like to open the pdb file as a text and find the charges in the binding site. Thanks!

[jbardhan]

Hi,

Can you please share more information about what you've done up to this point?

Have you downloaded the PDB file? When you say that you don't have the file location saved in your pymol, do you mean the APBS binary?

Thanks very much,
Jay

[ghost]

Hi Jay,

Thank you for getting back to me! I've uploaded a PDB file that I created from alphafolding an amino acid sequence + ligand into pymol, then used the APBS electrostatic plugin that is natively in pymol. That's where I'm up to right now, I've uploaded two screenshots of what the tool window looks like and the pymol visualization. I have the locations of the residues of the binding site; is there a way that APBS can also make a table-like file with the quantitative charges for those residues? Or the overall charge for the binding region? Thanks.

Best,
David

[jbardhan]

Thank you, those screenshots helped me understand better where you are in your efforts.

You asked, "I have the locations of the residues of the binding site; is there a way that APBS can also make a table-like file with the quantitative charges for those residues? Or the overall charge for the binding region?"

The APBS package solves the Poisson-Boltzmann equation to produce the electrostatic potential field shown in the plot you shared. To obtain the table and quantities you ask about, it will be much more effective to write a script in PyMOL using the selection tools. You might alternatively write some other kind of non-PyMOL script (shell/Python) that can read PDB/PQR files.

Does this help? I appreciate it doesn't give you a step-by-step solution within the APBS module of PyMOL.

Thanks very much,
Jay