I would recommend using the input file parameters generated by PDB2PQR as a starting point. In general, it is a good idea to have grid spacings at 0.5 A or smaller for visualization and at 0.25 A or smaller for energy calculations.
Pacific Northwest National Laboratory
From: sunyeping [mailto:firstname.lastname@example.org]
Sent: Monday, November 25, 2013 7:07 PM
Subject: [apbs-users] solvation energy
I want to calculate solvation energy of proteins. But I have no idea how to set the parameters dime and grid in the input file. There is an example for solvation energy: the Born ion. The dime and grid parameter given by the example are 97,97,97 and 0.33,0.33,0.33. Could anyone explain that how these values were set and how to set there parameters in the case of proteins. Thanks in advance.
Institute of Microbiology, Chinese Academy of Sciences