Dear Prof. Baker,
I am sorry for this delay!
It is still hard for me to understand those papers about electrostatic peak. However, my supervisor advised me today to calculate the local maximum/minimum potential within a certain area on the protein surface (or inside several grids) around the given residue as peak. As it is reported, a shell is drawn on the FDPB grid, using solvent points that are second nearest neighbor to molecule points, where the molecule is described with a solvent re-entrant surface, and the peak potential I need to calculate is the local extremum within 5% or 10% of the shell closest to the centre of a given residue. And he also said that I might not need the distance, for I just need to obtain the peak or average potential within a certain distance to a given residue to describe the electrostatic property of that residue.
Would you please help me to calculate the potential peak or give me some advice on how to extract the electrostatic property of a given residue from APBS output files? Thank you very much!
I attached the titles of two papers about this peak here, just in case that you are interested or that I didnt explain "peak" correctly:
Bate P, Warwicker J. Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods.
Greaves RWarwicker J. Active Site Identification through Geometry-based and Sequence Profile-based Calculations: Burial of Catalytic Clefts.
Thanks again and best wishes to you!
Sincerely yours,