Solvation Free Energy


! Copyright 2017 (Hiqmet Kamberaj)
! Calculates solvation energy of a (macro)molecule structure.
! Reference: R. Izairi and H. Kamberaj, A Comparison Study of Polar and Non-polar Contributions to Solvation Free Energy, 2017
! Written by H Kamberaj (moc.liamg|jarebmak.h#moc.liamg|jarebmak.h)
! This program is free software; you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation; either version 1 of the License, or
! (at your option) any later version.
! This program is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! GNU General Public License for more details.
! You should have received a copy of the GNU General Public License
! along with this program.
MMGBSA: A program written in Fortran90 for calculation of different contributions to solvation free energy (download):

  1. The van der Waals nonpolar term
  2. Generalized Born approximation electrostatic term
  3. Polar surface term
  4. Nonpolar surface term;

MMGBSA Modules:

mmgbsa.f90 - Main function
defs.f90 - MMGBSA definitions of constants and program data types, which are machine dependent
maths.f90 - Module of specific mathematical functions, which are machine dependent
iomodule.f90 - Module of Input/Output definition functions
msmodule.f90 - Module which includes functions for calculations of molecular surface
vdwmodule.f90 - Module which includes functions for calculations of non-polar van der Waals contribution
cavelecmodule.f90 - Module which includes functions for calculations of dielectric forces contribution
gbmodule.f90 - Module which includes functions for calculations of electrostatic contribution (GB method). This module has
also implemented distance dependence solute dielectric constant function.


./mmgbsa.exe /databasefolder/ outputname 2 80 0 300 1.4


argument 1 - Molecule dataset directory
argument 2 - Output file name + directory
argument 3 - Protein dielectric constant
argument 4 - Solvent dielectric constant
argument 5 - Ionic concentration
argument 6 - Temperature dielectric constant (in Kelvin)
argument 7 - Solvent probe radius in Angstrom

Data sets:

  1. Protein data set (charmm22 force field) (download);
  2. Small molecules data set (generalized amber force field) (download).
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