MM/PBSA method for GROMACS.
This project is maintained by RashmiKumari
polar = yes
This will allow the calculation of polar solvation energy. The value can change to “no” if one doesn’t want to do polar calculation.
cfac = 2
The factor by which molecular dimensions should expand to get a coarse grid dimensions. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).
fadd = 20
The amount (in Å) to add to molecular dimensions to get a fine grid dimensions. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).
gridspace = 0.2
It specifies the value (in Å) for fine grid spacing. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).
gmemceil = 4000
Usage: Sets memory (in MB) which will be used per-processor for a calculation. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).
PBsolver = npbe
This specifies whether linear or nonlinear Poisson Boltzmann equation should be solved. The accepted keywords are lpbe and npbe for linear and traditional non-linear PB equation, respectively. The effects of different value on the polar calculation is checked during this implementation.
mg-type = mg-auto
How multigrid PB calculation should be performed? Accepted keywords: mg-auto and mg-para.
mg-auto will perform automatically-configured sequential focusing multigrid PB calculation.
mg-para will perform automatically-configured parallel focusing multigrid PB calculation. Note: This keyword only works with external APBS executable and mpirun.
pcharge = 1
The charge of positive ions in bulk solution.
prad = 0.95
Radius of positive ions.
pconc = 0.150
Concentration of positive ion.
ncharge = -1
The charge of negative ions in bulk solution.
nrad = 1.81
Radius of negative ion.
nconc = 0.150
Concentration of negative ion.
pdie = 4
The value of solute dielectric constant. This can be change depending on the solute used for calculation. For highly charged solute high dielectric value will produce more accurate polar solvation energy.
sdie = 80
The value of solvent dielectric constant.
vdie = 1
The value of vacuum dielectric constant.
srad = 1.4
This specify the radius (in Å) of solvent molecules. This is used in case of probe-based surface definition. For more details, see Elec keyword srad here.
swin = 0.30
This specify the value for cubic spline window for spline-based surface definitions. Not used when probe-based surface are used in calculation. For more details, see Elec keyword swin here.
srfm = smol
This specify the model used to construct the dielectric and ion-accessibility coefficients. The accepted keywords are mol, smol, spl2 and spl4 and it may affect the polar energy calculation. For more details, see Elec keyword srfm here.
sdens = 10
Specify the number of grid points per Å2 for constructing the molecular surface or solvent accessible surface. Not taken in consideration when srad = 0.0 or srfm = spl2. For more details, see Elec keyword sdens here.
temp = 300
This specify the temperature used for Poisson-Boltzmann calculation. For more details, see Elec keyword temp here.
chgm = spl4
This specify the method used to map the biomolecular point charges to the grid for a multigrid Poisson-Boltzmann calculation. The accepted keywords are spl0, spl2 and spl4. The effects of these keywords on energy are not tested in this implementation. For more details, see Elec keyword chgm here.
bcfl = mdh
It specifies the type of boundary conditions used to solve the Poisson-Boltzmann equation. The accepted keywords are zero, sdh, mdh, focus, and map. However, use of focus, and map will terminate g_mmpbsa with error. The change in bcfl keywords may affect the polar energy calculation. The effects of these keywords on energy are not tested in this implementation. For more details, see Elec keyword bdfl here.