The MM_PBSA/GBSA approach represents the postprocessing method to evaluate free energies of binding or to calculate absolute free energies of molecules in solution. The sets of structures are usually collected with molecular dynamics or Monte Carlo methods. However, the collections of structures should be stored in the format of an AMBER trajectory file. The MM_PBSA/GBSA method combines the molecular mechanical energies with the continuum solvent approaches. The molecular mechanical energies are determined with the anal program from AMBER and represent the internal energy (bond, angle and dihedral), and van der Waals and electrostatic interactions. An infinite cutoff for all interactions is used. The electrostatic contribution to the solvation free energy is calculated with the Poisson-Boltzmann method implemented in DelPhi program [1]. Otherwise, the term can be calculated with the program GB kindly made available to us by Jayaram et al. [2], which uses the alternative approach utilizing the generalized Born equation to estimate the electrostatic contribution to the solvation free energy. The hydrophobic contribution to the solvation free energy is determined with solvent-accessible-surface-area- dependent term [3]. The binding free energies are evaluated according to the strategy described in references [4] and [5] . The contribution of the change to the conformational entropy during complex formation can be estimated with the nmode module from AMBER outside the mm_pbsa script.
The mm_pbsa script can be used to calculate the energies for a single molecule as well as a complex. In the latter case the mm_pbsa script uses the trajectory of the complex and calculates the respective energies for the complex and all interacting components by mapping the structures of the interacting molecules from that one of their complex. Thus, the assumption is made that no significant changes occur to the structures of the interacting molecules during the complex formation. However, when there is a such change to the structures, then three separate sets of trajectories should be collected for the individual interacting components which should be sampled alone in solution. These sets of trajectories should be processed individually with the mm_pbsa script which will produce files with the extension *.all.out. These files can be processed outside the mm_pbsa script with the program mm_pbsa_statistics_independent to extract all energy terms and interaction energies.
The mm_pbsa script can also calculate the energies for the interacting molecules and the binding free energies for their alanine/glycine mutants or other mutant produced by the two following schemes (i) when X-C-Y is mutated to H-C-H; and (ii) when C-X is mutated to C-H, if the topology of the interacting molecules permits such modification. The structures of the mutants are generated from the structures of the wild type, by the mapping procedure outlined in reference 5. The assumption is made that such modified sampling represents fairly well the distribution of the structures of the mutant. However, when the significant difference in sampling of the mutant and that one mapped from the wild type trajectory is expected, the mutant structures should be generated with the sampling techniques rather than the mapping procedure.
The user has to supply (i) the trajectory files; (ii) the
input files for the anal program, (iii) the topology files for
all interacting molecules without waters or their mutants,
depending of the purpose of the run. The samples of the input
files are supplied in the $AMBERHOME/src/mm_pbsa/EXAMPLE1 subdirectory.
Also, the user
has to provide the files with the charge and van der Waals
parameters for DelPhi and/or GB programs. Some parameter files
are supplied in the $AMBERHOME/src/mm_pbsa/PARAMETERS subdirectory.
The first ~ 410
lines of the mm_pbsa script represent documentation.
The mm_pbsa script can be used to identify the "hot" spots
in the interacting interfaces, to optimize the interacting
components for binding or stability and as a ranking procedure
in high throughput screening. The MM_PBSA/GBSA approach has
been successfully applied to study protein-peptide [5], protein-
protein (hormone-receptor) [6], protein-ligand [7], protein-nucleic
acid [8], nucleic acid-ligand [9] interactions, processes such as
protein folding [10] and the conformation-dependent free energies of
nucleic acids[4,11-12].