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[Licence| Download | New Version Template] aetq_v1_0.tar.gz(6908 Kbytes)
Manuscript Title: GMXPBSA 2.0: a GROMACS tool to perform MM/PBSA and computational alanine scanning
Authors: C. Paissoni, D. Spiliotopoulos, G. Musco, A. Spitaleri
Program title: GMXPBSA 2.0
Catalogue identifier: AETQ_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 185(2014)2920
Programming language: Bash, Perl.
Computer: Any computer.
Operating system: Linux, Unix OS.
RAM: ~ 2 Gbytes
Keywords: Molecular dynamics simulation, Binding Free Energy, Virtual screening, GROMACS, Computational Alanine Scanning, MM/PBSA.
Classification: 3.

External routines: APBS (http://www.poissonboltzmann.org/apbs/) and GROMACS installations (http://www.gromacs.org). Optionally LaTeX.

Nature of problem:
Calculates the Molecular Mechanics (MM) data (Lennard-Jones and Coulomb terms) and the solvation energy terms (polar and nonpolar terms respectively) from an ensemble of structures derived from GROMACS molecular dynamics simulation trajectory. These calculations are performed for each single component of the simulated complex, including protein and ligand. In order to cancel out artefacts an identical grid setup for each component, including complex, protein and ligand, is required. Performs statistical analysis on the extracted data and comparison with wild-type complex in case of either computational alanine scanning or calculations on a set of simulations. Evaluates possible outliers in the frames extracted from the simulations during the binding free energy calculations.

Solution method:
The tool combines the freely available programs GROMACS and APBS to:
  1. extract frames from a single or multiple complex molecular dynamics (MD) simulation, allowing comparison between multiple trajectories;
  2. split the complex frames in the single components including complex, protein and ligand;
  3. calculate the Lennard-Jones and Coulomb energy values (MM terms);
  4. calculate the polar solvation energy values using the implicit solvation Poisson-Boltzmann model (PB);
  5. calculate the nonpolar solvation energy value based on the solvent accessible surface area (SASA);
  6. combine all the calculated terms into the final binding free energy value;
  7. repeat the same procedure from point 1 to 6 for each simulation in case of computational alanine scanning (CAS) or simultaneous comparison of different MDs.

Restrictions:
Input format files compatible with GROMACS engine 4.5 and later versions. Availability of the force field or of the topology files.

Running time:
On a single core, Lennard-Jones, Coulomb and nonpolar solvation terms calculations require a few minutes. The time required for polar solvation terms calculations depends on the system size.