I am getting incorrect ionization states for my ligands. I have set up a protocol in which I ionize my ligands within the Ligand preparation component (by setting min and max pH to 7).
The protocol works as expected - It protonates or deprotonates atoms based on the computed pKa value. The problem actually lies in pKa calculation : Using the pKa calculator component, I figured out that the values are computed wrongly (I confirmed this by obtaining the pKa values from two other independent sources for several ligands).
I am aware that there is an option to provide some example molecules with pKa values to make the prediction better. However, I am unable to find in my public/data/pKa directory, a directory named "AcidBaseSites" or "Models" or any example files. Am I missing files from my installation that are causing incorrect pKa values? If yes, then what would be the remedy? If not, then can you please suggest what am I doing wrong? Thanks in advance.
The protocol works as expected - It protonates or deprotonates atoms based on the computed pKa value. The problem actually lies in pKa calculation : Using the pKa calculator component, I figured out that the values are computed wrongly (I confirmed this by obtaining the pKa values from two other independent sources for several ligands).
I am aware that there is an option to provide some example molecules with pKa values to make the prediction better. However, I am unable to find in my public/data/pKa directory, a directory named "AcidBaseSites" or "Models" or any example files. Am I missing files from my installation that are causing incorrect pKa values? If yes, then what would be the remedy? If not, then can you please suggest what am I doing wrong? Thanks in advance.
