1debug: Input string: 2read 3 mol pqr ion.pqr 4end 5 6elec name elec 7mg-manual 8dime 33 33 33 9grid 0.500 0.500 0.500 10# nlev 4 11gcent mol 1 12ion charge 1.000 conc 0.150 radius 2.000 13ion charge -1.000 conc 0.150 radius 2.000 14pdie 2.000 15sdie 78.540 16srad 1.400 17swin 0.300 18temp 298.150 19sdens 10.000 20mol 1 21chgm spl2 22lpbe 23bcfl sdh 24srfm spl2 25calcenergy total 26calcforce total 27end 28 29apolar name npolar 30bconc 0.0 31press 0.0 32dpos 0.2 33mol 1 34srfm sacc 35grid 0.2 0.2 0.2 36gamma 0.105 37srad 1.400 38swin 0.300 39temp 298.150 40sdens 10.000 41calcenergy total 42calcforce comps 43end 44 45 46quit 47 48Parsed input string. 49Preparing to run 2 PBE calculations. 50---------------------------------------- 51CALCULATION #1 (elec): MULTIGRID 52 Setting up problem... 53 Using cubic spline charge discretization. 54 Grid dimensions: 33 x 33 x 33 55 Grid spacings: 0.500 x 0.500 x 0.500 56 Grid lengths: 16.000 x 16.000 x 16.000 57 Grid center: (4.681, 3.930, -0.620) 58 Multigrid levels: 4 59 Molecule ID: 1 60 Linearized traditional PBE 61 Single Debye-Huckel sphere boundary conditions 62 2 ion species (0.150 M ionic strength): 63 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 64 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 65 Solute dielectric: 2.000 66 Solvent dielectric: 78.540 67 Using spline-based surface definition;window = 0.300 68 Temperature: 298.150 K 69 Electrostatic energies will be calculated 70 Net solvent forces will be calculated 71---------------------------------------- 72CALCULATION #2 (npolar): APOLAR 73---------------------------------------- 74Final memory usage: 0.001 MB total, 8.547 MB high water 75Reading parameter file apbs-forces-tot.in 76 Reading PQR file ... 77Mol. dimensions: 6.386 4.868 5.895 78 Grid dime not specified, calculating ... 79 Grid values: 80fglen: 26.386 24.868 25.895 81cglen: 26.386 24.868 25.895 82dime: 33 33 33 83grid: 0.500 0.500 0.500 84Required memory (in MB): 6.854 85 PQR file (x, y, z, charge, radius): 86 1 3.555 3.970 -0.000 -0.416 1.824 87 2 2.733 4.556 -0.000 0.272 0.600 88 3 4.853 4.614 -0.000 0.034 1.908 89 4 5.408 4.316 0.890 0.082 1.387 90 5 5.661 4.221 -1.232 -0.182 1.908 91 6 5.123 4.521 -2.131 0.060 1.487 92 7 6.630 4.719 -1.206 0.060 1.487 93 8 5.809 3.141 -1.241 0.060 1.487 94 i_param: 95calc_type 0 96nlev 4 97cmeth 1 98ccmeth 1 99fcmeth 1 100chgm 1 101nonlin 0 102bcfl 1 103srfm 2 104calcenergy 1 105calcforce 1 106wpot 0 107wchg 0 108wsmol 0 109wkappa 0 110wdiel 0 111watompot 0 112rpot 0 1130 0 114calcnpforce 2 115calcnpenergy 1 116nion 2 117rchg 0 118rkappa 0 119rdiel 0 120 r_param: 121pdie 2.000 122 main.f: apbs return code: 0 123esenergy (kJ/mol): 150.87575187 124npenergy (kJ/mol): 22.80602401 125esenergy (kcal/mol): 36.06017001 126npenergy (kcal/mol): 5.45077054 127 main: Total force on molecule kJ/(mol/A) 128qf -58.07701165 40.45922947 57.50773299 129ib 0.00014582 0.00025737 -0.00002647 130db 9.74780014 -2.44894324 -1.03462148 131pol -48.32906569 38.01054360 56.47308504 132apol 43.94102579 24.67825906 -15.48817878 133tot -4.38803990 62.68880266 40.98490626 134