I probably didn't make myself clear in my last email.
What I meant is that there is an option in pymol APBS tool that allows one to use pymol to generate pqr file from pdb file, instead of loading an pqr file generated externally. I noticed that the electrostatic potential looks quite different for the pqr file of the same structure generated on pdb2pqr server. My question is how does pymol assign partial charges? I can only find a file called apbs_tools.py under the directory of ./modules/pmg_tk/startup/ that remotely has some information.
When one uses the APBS plugin of pymol to generate a pqr file, how
dose it assign the partial charges to the atoms, what force field is
it based on? Thank you.