Dear APBS users,
I am going to perform a series of calculations using APBS to understand the contributions of salt bridges at the interface of a protein homodimer to the free energy of binding (dimerisation).
By reading the litterature I have seen that many have used a finite element method to solve PBE. They perform a refinement to a first lower resolution calculation in which the boundary points are away 20A from the molecule; the refinement step consists in a focusing calculation in which the boundary points are closer to the molecule with an increase of grid resolution.
However, reading at the APBS manual seems that a focusing calculation can be also done using a multigrid method (mg-manual) rather than of a finite element one.
I want to compute the contribution (in terms of free energy) of the salt bridges to the dimer formation by replacing the charged residues by hydrophobic isosteres.
Can you please advise if "mg-manual" suits the purposes of my study?
Do I need to prepare two input files in which the keyword bcfl has as the argument "mdh" and a second input file in which the keyword is "focus" with the new values for the boundary?
Any help will be much appreciated.
Davide Mercadante - PhD student -
Department of Chemistry
The University of Auckland
Rm 438 ext. 89171
1142 Auckland, New Zealand