From: Assa Sittner <assaz@wi...>  20050609 22:43:03

Hi, i'm trying to calculate solvation energies of a protein in two different conformations, and i've got a few questions, and excuse me if they're stupid (today's the 3rd day i'm using apbs): 1. as i know it, and correct me if i'm wrong, i have to calculate , (for each conformation in my case), the difference in total energy energy between the "solvated protein" (using solvent dielectric) and the protein in vacuo. i did it, using different grid spacing, and received interesting results: 1. for two grids with the same size but different spacing, i have performed a solvation calculation (=totEsolvtotEvacuo), i received different absolute results for total energy(totEsolv and totEvacuo), but the solvation energies (=totEsolvtotEvacuo) stayed very close in both grid resolutions. i understand that there are artifacts, due to the discrete nature of the grid, but are they so strong? here are the figures: in both cases i used Grid lengths: 58.761 x 32.129 x 25.828 in which the protein fits very comfortably. for a 161 x 97 x 97 grid: totEsolv =9.534619136962E+04 kJ/mol totEvacuo =9.875123989039E+04 kJ/mol totEsolvtotEvacuo= 0.340504852 E+04 kJ/mol for a 161 x 129 x 129 grid : totEsolv = 6.803247450678E+04 kJ/mol totEvacuo = 7.141364011794E+04 kJ/mol totEsolvtotEvacuo=0.338116561 E+04 kJ/mol i read some posting about it, that said that the coulombic energy should be added: http://cholla.wustl.edu/pipermail/apbsusers/2003October/000104.html can anyone give me a little deeper explanation about why it's done, and how can this correction be gridresolutiondependant (since i need a different correction for each grid obviously)?is there also an effect of grid size (for a given spacing), because of the larget solvent volume? 2. what is a legitimate grid spacing (in angstroms) for calculations, in order for the to be meaningful (but not necessarily very accurate)? 3. how can i estimate the error, in the energy calculations? (except for running many calculations for different orientations on the molecule) thanks a lot in advance, T 