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apolar_sasa.mdp
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apolar_sasa.mdp
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;Polar calculation: "yes" or "no"
polar = no
;=============
;PSIZE options
;=============
;Factor by which to expand molecular dimensions to get coarsegrid dimensions.
cfac = 1.5
;The desired fine mesh spacing (in A)
gridspace = 0.5
:Amount (in A) to add to molecular dimensions to get fine grid dimensions.
fadd = 5
;Maximum memory (in MB) available per-processor for a calculation.
gmemceil = 4000
;=============================================
;APBS keywords for polar solvation calculation
;=============================================
;Way to perform calculations (sequential or parallel)
mg-type = mg-auto
;Charge of positive ions
pcharge = 1
;Radius of positive charged ions
prad = 0.95
;Concentration of positive charged ions
pconc = 0.150
;Charge of negative ions
ncharge = -1
;Radius of negative charged ions
nrad = 1.81
;Concentration of negative charged ions
nconc = 0.150
;Solute dielectric constant
pdie = 2
;Solvent dielectric constant
sdie = 80
;Reference or vacuum dielectric constant
vdie = 1
;Solvent probe radius
srad = 1.4
;Method used to map biomolecular charges on grid. chgm = spl0 or spl2 or spl4
chgm = spl4
;Model used to construct dielectric and ionic boundary. srfm = smol or spl2 or spl4
srfm = smol
;Value for cubic spline window. Only used in case of srfm = spl2 or spl4.
swin = 0.30
;Numebr of grid point per A^2. Not used when (srad = 0.0) or (srfm = spl2 or spl4)
sdens = 10
;Temperature in K
temp = 300
;Type of boundary condition to solve PB equation. bcfl = zero or sdh or mdh or focus or map
bcfl = mdh
;Non-linear (npbe) or linear (lpbe) PB equation to solve
PBsolver = lpbe
;========================================================
;APBS kwywords for Apolar/Non-polar solvation calculation
;========================================================
;Non-polar solvation calculation: "yes" or "no"
apolar = yes
;Repulsive contribution to Non-polar
;===SASA model ====
;Gamma (Surface Tension) kJ/(mol A^2)
gamma = 0.0226778
;Probe radius for SASA (A)
sasrad = 1.4
;Offset (c) kJ/mol
sasaconst = 3.84928
;===SAV model===
;Pressure kJ/(mol A^3)
press = 0
;Probe radius for SAV (A)
savrad = 0
;Offset (c) kJ/mol
savconst = 0
;Attractive contribution to Non-polar
;===WCA model ====
;using WCA method: "yes" or "no"
WCA = no
;Probe radius for WCA
wcarad = 1.20
;bulk solvent density in A^3
bconc = 0.033428
;displacment in A for surface area derivative calculation
dpos = 0.05
;Quadrature grid points per A for molecular surface or solvent accessible surface
APsdens = 20
;Quadrature grid spacing in A for volume integral calculations
grid = 0.45 0.45 0.45
;Parameter to construct solvent related surface or volume
APsrfm = sacc
;Cubic spline window in A for spline based surface definitions
APswin = 0.3
;Temperature in K
APtemp = 300