1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
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##########################################################################
### ION-ION PMF
### $Id: apbs.in 1100 2007-06-25 17:02:52Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
##########################################################################
read
mol pdb complex.pdb
parm flat parm.dat
end
elec name solv
mg-manual
dime 65 65 65
nlev 4
grid 0.21 0.21 0.21
gcent 0.0 0.0 0.0
mol 1
lpbe
bcfl mdh
pdie 1.0
sdie 78.54
chgm spl2
srfm spl2
srad 1.4
swin 0.3
sdens 10.0
temp 298.15
calcenergy total
calcforce comps
end
elec name ref
mg-manual
dime 65 65 65
nlev 4
grid 0.21 0.21 0.21
gcent 0.0 0.0 0.0
mol 1
lpbe
bcfl mdh
pdie 1.0
sdie 1.0
chgm spl2
srfm spl2
srad 1.4
swin 0.3
sdens 10.0
temp 298.15
calcenergy total
calcforce comps
end
apolar name asolv
grid 0.1 0.1 0.1
mol 1
srfm sacc
swin 0.3
srad 1.4
press 0.00
gamma 0.00072
bconc 0.033
sdens 100.0
dpos 0.2
temp 298.15
calcenergy total
calcforce comps
end
# THIS GIVES THE POLAR SOLVATION ENERGY OF THE COMPLEX
print elecEnergy solv - ref end
# THIS GIVES THE POLAR SOLVATION FORCES ON THE COMPLEX
print elecForce solv - ref end
# THIS GIVES THE APOLAR SOLVATION ENERGY OF THE COMPLEX
print apolEnergy asolv end
# THIS GIVES THE APOLAR SOLVATION FORCES ON THE COMPLEX
print apolForce asolv end
quit
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