Can you please provide more information about what you are trying to calculate? For most quantitative calculations (as opposed to visualization), it is a good idea to have the grid spacing less than 0.5 A (often ~0.25 A). The grid length has a more complicated formula; I recommend using PDB2PQR to generate template input files that can recommend grid lengths.
Pacific Northwest National Laboratory
From: Javier Cáceres [mailto:jav.cdp@...]
Sent: Friday, August 30, 2013 7:17 AM
Subject: [apbs-users] Set correct grid values
Im new on apbs. I want to make electrostatic binding energy calculations, and a have doubts on what are good values for the grid dimensions.
I really want to know when my calculations are set in the right way, and the values that a put in the input file are the corrects for my protein.
For example, I don't understand what dime values are the best for my protein. A put 321 321 321 and I get a result, but when a put 289 257 289 a get other. Wich one is the best? How do I know?