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The input file

Description

xBFreE (MMPBSA) input file contains all the specifications for the MMPBSA calculations. The input file is syntactically similar to other programs in Amber, although we have incorporated format more similar to that of GROMACS *.mdp files (see below). The input file contains sections called namelist where the variables are defined for each calculation. The allowed namelists are:

  • &general: contains variables that apply to all aspects of the calculation or parameters required for building AMBER topologies.
  • &gb: unique variables to Generalized Born (GB) calculations.
  • &gbnsr6: unique variables to GBNSR6 calculations.
  • &pb: unique variables to Poisson Boltzmann (PB) calculations.
  • &rism: unique variables to 3D-RISM calculations.
  • &alanine_scanning: unique variables to alanine scanning calculations.
  • &decomp: unique variables to the decomposition scheme.
  • &nmode: unique variables to the normal mode (NMODE) calculations used to approximate vibrational entropies.

Generation of input files with xBFreE

The input file can be created using xBFreE by selecting the subcommand and the calculations you want to perform.

Note

Note that the command-line is basically the same for all MD programs. They only differ in the subcommand selected according to the MD program.

Command-line
xbfree gmx_MMPBSA --create_input args
where args can be: gb, gbnsr6, pb, rism, ala, decomp, nmode, all

Example:

xbfree gmx_MMPBSA --create_input gb

xbfree gmx_MMPBSA --create_input pb

xbfree gmx_MMPBSA --create_input gb pb decomp

xbfree gmx_MMPBSA --create_input

or 

xbfree gmx_MMPBSA --create_input all

Command-line
xbfree amber_MMPBSA --create_input args
where args can be: gb, gbnsr6, pb, rism, ala, decomp, nmode, all

Example:

xbfree amber_MMPBSA --create_input gb

xbfree amber_MMPBSA --create_input pb

xbfree amber_MMPBSA --create_input gb pb decomp

xbfree amber_MMPBSA --create_input

or 

xbfree amber_MMPBSA --create_input all

Command-line
xbfree namd_MMPBSA --create_input args
where args can be: gb, gbnsr6, pb, rism, ala, decomp, nmode, all

Example:

xbfree namd_MMPBSA --create_input gb

xbfree namd_MMPBSA --create_input pb

xbfree namd_MMPBSA --create_input gb pb decomp

xbfree namd_MMPBSA --create_input

or 

xbfree namd_MMPBSA --create_input all

Command-line
xbfree charmm_MMPBSA --create_input args
where args can be: gb, gbnsr6, pb, rism, ala, decomp, nmode, all

Example:

xbfree charmm_MMPBSA --create_input gb

xbfree charmm_MMPBSA --create_input pb

xbfree charmm_MMPBSA --create_input gb pb decomp

xbfree charmm_MMPBSA --create_input

or 

xbfree charmm_MMPBSA --create_input all

Danger

  • Note that several variables must be explicitly defined in the input file
  • Performing all the calculations in the same run can take a long time
2023-11-10 2023-11-10