Fri Mar 2 14:29:49 PST 2012 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph_thinner.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Mar 2 2012 at 14:29:49 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: ILE 3 has a net charge of -0.2480 !!! WARNING: MET 4 has a net charge of -0.2480 !!! WARNING: GLY 5 has a net charge of -0.2480 !!! WARNING: SER 6 has a net charge of -0.5580 !!! WARNING: SER 7 has a net charge of -0.5580 !!! WARNING: VAL 8 has a net charge of -0.2480 !!! WARNING: TYR 9 has a net charge of -0.5870 !!! WARNING: ILE 10 has a net charge of -0.2480 !!! WARNING: THR 11 has a net charge of -0.5580 !!! WARNING: VAL 12 has a net charge of -0.2480 !!! WARNING: GLU 13 has a net charge of -1.2480 !!! WARNING: LEU 14 has a net charge of -0.2480 !!! WARNING: ALA 15 has a net charge of -0.2480 !!! WARNING: ILE 16 has a net charge of -0.2480 !!! WARNING: ALA 17 has a net charge of -0.2480 !!! WARNING: VAL 18 has a net charge of -0.2480 !!! WARNING: LEU 19 has a net charge of -0.2480 !!! WARNING: ALA 20 has a net charge of -0.2480 !!! WARNING: ILE 21 has a net charge of -0.2480 !!! WARNING: LEU 22 has a net charge of -0.2480 !!! WARNING: GLY 23 has a net charge of -0.2480 !!! WARNING: ASN 24 has a net charge of -0.9360 !!! WARNING: VAL 25 has a net charge of -0.2480 !!! WARNING: LEU 26 has a net charge of -0.2480 !!! WARNING: VAL 27 has a net charge of -0.2480 !!! WARNING: CYS 28 has a net charge of -0.3830 !!! WARNING: TRP 29 has a net charge of -0.5420 !!! WARNING: ALA 30 has a net charge of -0.2480 !!! WARNING: VAL 31 has a net charge of -0.2480 !!! WARNING: TRP 32 has a net charge of -0.5420 !!! WARNING: LEU 33 has a net charge of -0.2480 !!! WARNING: ASN 34 has a net charge of -0.9360 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: ASN 36 has a net charge of -0.9360 !!! WARNING: LEU 37 has a net charge of -0.2480 !!! WARNING: GLN 38 has a net charge of -0.9360 !!! WARNING: ASN 39 has a net charge of -0.9360 !!! WARNING: VAL 40 has a net charge of -0.2480 !!! WARNING: THR 41 has a net charge of -0.5580 !!! WARNING: ASN 42 has a net charge of -0.9360 !!! WARNING: TYR 43 has a net charge of -0.5870 !!! WARNING: PHE 44 has a net charge of -0.2480 !!! WARNING: VAL 45 has a net charge of -0.2480 !!! WARNING: VAL 46 has a net charge of -0.2480 !!! WARNING: SER 47 has a net charge of -0.5580 !!! WARNING: LEU 48 has a net charge of -0.2480 !!! WARNING: ALA 49 has a net charge of -0.2480 !!! WARNING: ALA 50 has a net charge of -0.2480 !!! WARNING: ALA 51 has a net charge of -0.2480 !!! WARNING: ASP 52 has a net charge of -1.2480 !!! WARNING: ILE 53 has a net charge of -0.2480 !!! WARNING: ALA 54 has a net charge of -0.2480 !!! WARNING: VAL 55 has a net charge of -0.2480 !!! WARNING: GLY 56 has a net charge of -0.2480 !!! WARNING: VAL 57 has a net charge of -0.2480 !!! WARNING: LEU 58 has a net charge of -0.2480 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: ILE 60 has a net charge of -0.2480 !!! WARNING: PHE 62 has a net charge of -0.2480 !!! WARNING: ALA 63 has a net charge of -0.2480 !!! WARNING: ILE 64 has a net charge of -0.2480 !!! WARNING: THR 65 has a net charge of -0.5580 !!! WARNING: ILE 66 has a net charge of -0.2480 !!! WARNING: SER 67 has a net charge of -0.5580 !!! WARNING: THR 68 has a net charge of -0.5580 !!! WARNING: GLY 69 has a net charge of -0.2480 !!! WARNING: PHE 70 has a net charge of -0.2480 !!! WARNING: CYX 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: ALA 73 has a net charge of -0.2480 !!! WARNING: CYX 74 has a net charge of -0.2480 !!! WARNING: HIE 75 has a net charge of -0.5680 !!! WARNING: GLY 76 has a net charge of -0.2480 !!! WARNING: CYX 77 has a net charge of -0.2480 !!! WARNING: LEU 78 has a net charge of -0.2480 !!! WARNING: PHE 79 has a net charge of -0.2480 !!! WARNING: ILE 80 has a net charge of -0.2480 !!! WARNING: ALA 81 has a net charge of -0.2480 !!! WARNING: CYS 82 has a net charge of -0.3830 !!! WARNING: PHE 83 has a net charge of -0.2480 !!! WARNING: VAL 84 has a net charge of -0.2480 !!! WARNING: LEU 85 has a net charge of -0.2480 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: LEU 87 has a net charge of -0.2480 !!! WARNING: THR 88 has a net charge of -0.5580 !!! WARNING: GLN 89 has a net charge of -0.9360 !!! WARNING: SER 90 has a net charge of -0.5580 !!! WARNING: SER 91 has a net charge of -0.5580 !!! WARNING: ILE 92 has a net charge of -0.2480 !!! WARNING: PHE 93 has a net charge of -0.2480 !!! WARNING: SER 94 has a net charge of -0.5580 !!! WARNING: LEU 95 has a net charge of -0.2480 !!! WARNING: LEU 96 has a net charge of -0.2480 !!! WARNING: ALA 97 has a net charge of -0.2480 !!! WARNING: ILE 98 has a net charge of -0.2480 !!! WARNING: ALA 99 has a net charge of -0.2480 !!! WARNING: ILE 100 has a net charge of -0.2480 !!! WARNING: ASP 101 has a net charge of -1.2480 !!! WARNING: ARG 102 has a net charge of -0.9880 !!! WARNING: TYR 103 has a net charge of -0.5870 !!! WARNING: ILE 104 has a net charge of -0.2480 !!! WARNING: ALA 105 has a net charge of -0.2480 !!! WARNING: ILE 106 has a net charge of -0.2480 !!! WARNING: ARG 107 has a net charge of -0.9880 !!! WARNING: ILE 108 has a net charge of -0.2480 !!! WARNING: LEU 110 has a net charge of -0.2480 !!! WARNING: ARG 111 has a net charge of -0.9880 !!! WARNING: TYR 112 has a net charge of -0.5870 !!! WARNING: ASN 113 has a net charge of -0.9360 !!! WARNING: GLY 114 has a net charge of -0.2480 !!! WARNING: LEU 115 has a net charge of -0.2480 !!! WARNING: VAL 116 has a net charge of -0.2480 !!! WARNING: THR 117 has a net charge of -0.5580 !!! WARNING: GLY 118 has a net charge of -0.2480 !!! WARNING: THR 119 has a net charge of -0.5580 !!! WARNING: ARG 120 has a net charge of -0.9880 !!! WARNING: ALA 121 has a net charge of -0.2480 !!! WARNING: LYS 122 has a net charge of -0.1810 !!! WARNING: GLY 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: ILE 125 has a net charge of -0.2480 !!! WARNING: ALA 126 has a net charge of -0.2480 !!! WARNING: ILE 127 has a net charge of -0.2480 !!! WARNING: CYS 128 has a net charge of -0.3830 !!! WARNING: TRP 129 has a net charge of -0.5420 !!! WARNING: VAL 130 has a net charge of -0.2480 !!! WARNING: LEU 131 has a net charge of -0.2480 !!! WARNING: SER 132 has a net charge of -0.5580 !!! WARNING: PHE 133 has a net charge of -0.2480 !!! WARNING: ALA 134 has a net charge of -0.2480 !!! WARNING: ILE 135 has a net charge of -0.2480 !!! WARNING: GLY 136 has a net charge of -0.2480 !!! WARNING: LEU 137 has a net charge of -0.2480 !!! WARNING: THR 138 has a net charge of -0.5580 !!! WARNING: MET 140 has a net charge of -0.2480 !!! WARNING: LEU 141 has a net charge of -0.2480 !!! WARNING: GLY 142 has a net charge of -0.2480 !!! WARNING: TRP 143 has a net charge of -0.5420 !!! WARNING: ASN 144 has a net charge of -0.9360 !!! WARNING: ASN 145 has a net charge of -0.9360 !!! WARNING: CYX 146 has a net charge of -0.2480 !!! WARNING: GLY 147 has a net charge of -0.2480 !!! WARNING: GLN 148 has a net charge of -0.9360 !!! WARNING: SER 156 has a net charge of -0.5580 !!! WARNING: GLN 157 has a net charge of -0.9360 !!! WARNING: GLY 158 has a net charge of -0.2480 !!! WARNING: CYX 159 has a net charge of -0.2480 !!! WARNING: GLY 160 has a net charge of -0.2480 !!! WARNING: GLU 161 has a net charge of -1.2480 !!! WARNING: GLY 162 has a net charge of -0.2480 !!! WARNING: GLN 163 has a net charge of -0.9360 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: ALA 165 has a net charge of -0.2480 !!! WARNING: CYX 166 has a net charge of -0.2480 !!! WARNING: LEU 167 has a net charge of -0.2480 !!! WARNING: PHE 168 has a net charge of -0.2480 !!! WARNING: GLU 169 has a net charge of -1.2480 !!! WARNING: ASP 170 has a net charge of -1.2480 !!! WARNING: VAL 171 has a net charge of -0.2480 !!! WARNING: VAL 172 has a net charge of -0.2480 !!! WARNING: MET 174 has a net charge of -0.2480 !!! WARNING: ASN 175 has a net charge of -0.9360 !!! WARNING: TYR 176 has a net charge of -0.5870 !!! WARNING: MET 177 has a net charge of -0.2480 !!! WARNING: VAL 178 has a net charge of -0.2480 !!! WARNING: TYR 179 has a net charge of -0.5870 !!! WARNING: PHE 180 has a net charge of -0.2480 !!! WARNING: ASN 181 has a net charge of -0.9360 !!! WARNING: PHE 182 has a net charge of -0.2480 !!! WARNING: PHE 183 has a net charge of -0.2480 !!! WARNING: ALA 184 has a net charge of -0.2480 !!! WARNING: CYS 185 has a net charge of -0.3830 !!! WARNING: VAL 186 has a net charge of -0.2480 !!! WARNING: LEU 187 has a net charge of -0.2480 !!! WARNING: VAL 188 has a net charge of -0.2480 !!! WARNING: LEU 190 has a net charge of -0.2480 !!! WARNING: LEU 191 has a net charge of -0.2480 !!! WARNING: LEU 192 has a net charge of -0.2480 !!! WARNING: MET 193 has a net charge of -0.2480 !!! WARNING: LEU 194 has a net charge of -0.2480 !!! WARNING: GLY 195 has a net charge of -0.2480 !!! WARNING: VAL 196 has a net charge of -0.2480 !!! WARNING: TYR 197 has a net charge of -0.5870 !!! WARNING: LEU 198 has a net charge of -0.2480 !!! WARNING: ARG 199 has a net charge of -0.9880 !!! WARNING: ILE 200 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: LEU 202 has a net charge of -0.2480 !!! WARNING: ALA 203 has a net charge of -0.2480 !!! WARNING: ALA 204 has a net charge of -0.2480 !!! WARNING: ARG 205 has a net charge of -0.9880 !!! WARNING: ARG 206 has a net charge of -0.9880 !!! WARNING: GLN 207 has a net charge of -0.9360 !!! WARNING: LEU 208 has a net charge of -0.2480 !!! WARNING: ARG 222 has a net charge of -0.9880 !!! WARNING: SER 223 has a net charge of -0.5580 !!! WARNING: THR 224 has a net charge of -0.5580 !!! WARNING: LEU 225 has a net charge of -0.2480 !!! WARNING: GLN 226 has a net charge of -0.9360 !!! WARNING: LYS 227 has a net charge of -0.1810 !!! WARNING: GLU 228 has a net charge of -1.2480 !!! WARNING: VAL 229 has a net charge of -0.2480 !!! WARNING: HIE 230 has a net charge of -0.5680 !!! WARNING: ALA 231 has a net charge of -0.2480 !!! WARNING: ALA 232 has a net charge of -0.2480 !!! WARNING: LYS 233 has a net charge of -0.1810 !!! WARNING: SER 234 has a net charge of -0.5580 !!! WARNING: LEU 235 has a net charge of -0.2480 !!! WARNING: ALA 236 has a net charge of -0.2480 !!! WARNING: ILE 237 has a net charge of -0.2480 !!! WARNING: ILE 238 has a net charge of -0.2480 !!! WARNING: VAL 239 has a net charge of -0.2480 !!! WARNING: GLY 240 has a net charge of -0.2480 !!! WARNING: LEU 241 has a net charge of -0.2480 !!! WARNING: PHE 242 has a net charge of -0.2480 !!! WARNING: ALA 243 has a net charge of -0.2480 !!! WARNING: LEU 244 has a net charge of -0.2480 !!! WARNING: CYS 245 has a net charge of -0.3830 !!! WARNING: TRP 246 has a net charge of -0.5420 !!! WARNING: LEU 247 has a net charge of -0.2480 !!! WARNING: LEU 249 has a net charge of -0.2480 !!! WARNING: HIE 250 has a net charge of -0.5680 !!! WARNING: ILE 251 has a net charge of -0.2480 !!! WARNING: ILE 252 has a net charge of -0.2480 !!! WARNING: ASN 253 has a net charge of -0.9360 !!! WARNING: CYS 254 has a net charge of -0.3830 !!! WARNING: PHE 255 has a net charge of -0.2480 !!! WARNING: THR 256 has a net charge of -0.5580 !!! WARNING: PHE 257 has a net charge of -0.2480 !!! WARNING: PHE 258 has a net charge of -0.2480 !!! WARNING: CYX 259 has a net charge of -0.2480 !!! WARNING: ASP 261 has a net charge of -1.2480 !!! WARNING: CYX 262 has a net charge of -0.2480 !!! WARNING: SER 263 has a net charge of -0.5580 !!! WARNING: HIP 264 has a net charge of -0.2120 !!! WARNING: ALA 265 has a net charge of -0.2480 !!! WARNING: LEU 267 has a net charge of -0.2480 !!! WARNING: TRP 268 has a net charge of -0.5420 !!! WARNING: LEU 269 has a net charge of -0.2480 !!! WARNING: MET 270 has a net charge of -0.2480 !!! WARNING: TYR 271 has a net charge of -0.5870 !!! WARNING: LEU 272 has a net charge of -0.2480 !!! WARNING: ALA 273 has a net charge of -0.2480 !!! WARNING: ILE 274 has a net charge of -0.2480 !!! WARNING: VAL 275 has a net charge of -0.2480 !!! WARNING: LEU 276 has a net charge of -0.2480 !!! WARNING: SER 277 has a net charge of -0.5580 !!! WARNING: THR 279 has a net charge of -0.5580 !!! WARNING: ASN 280 has a net charge of -0.9360 !!! WARNING: SER 281 has a net charge of -0.5580 !!! WARNING: VAL 282 has a net charge of -0.2480 !!! WARNING: VAL 283 has a net charge of -0.2480 !!! WARNING: ASN 284 has a net charge of -0.9360 !!! WARNING: PHE 286 has a net charge of -0.2480 !!! WARNING: ILE 287 has a net charge of -0.2480 !!! WARNING: TYR 288 has a net charge of -0.5870 !!! WARNING: ALA 289 has a net charge of -0.2480 !!! WARNING: TYR 290 has a net charge of -0.5870 !!! WARNING: ARG 291 has a net charge of -0.9880 !!! WARNING: ILE 292 has a net charge of -0.2480 !!! WARNING: ARG 293 has a net charge of -0.9880 !!! WARNING: GLU 294 has a net charge of -1.2480 !!! WARNING: PHE 295 has a net charge of -0.2480 !!! WARNING: ARG 296 has a net charge of -0.9880 !!! WARNING: GLN 297 has a net charge of -0.9360 !!! WARNING: THR 298 has a net charge of -0.5580 !!! WARNING: PHE 299 has a net charge of -0.2480 !!! WARNING: ARG 300 has a net charge of -0.9880 !!! WARNING: LYS 301 has a net charge of -0.1810 !!! WARNING: ILE 302 has a net charge of -0.2480 !!! WARNING: ILE 303 has a net charge of -0.2480 !!! WARNING: ARG 304 has a net charge of -0.9880 !!! WARNING: SER 305 has a net charge of -0.5580 !!! WARNING: HIE 306 has a net charge of -0.5680 !!! WARNING: VAL 307 has a net charge of -0.2480 !!! WARNING: LEU 308 has a net charge of -0.2480 !!! WARNING: ARG 309 has a net charge of -0.9880 !!! WARNING: GLN 310 has a net charge of -0.9360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4842022 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -32.54400 15.91000 ymin,ymax (A): -36.44200 24.72600 zmin,zma (A): 6.767000 80.29000 x,y,z range (A): 48.45400 61.16800 73.52300 scale (grids/A): 0.4842022 object centre (A): -8.316999 -5.858001 43.52850 number of atom coordinates read : 2366 total number of charged atoms : 2235 net assigned charge : -119.1277 assigned positive charge : 275.7153 centred at (gu) : 90.89350 88.95951 87.54330 assigned negative charge : -394.8429 centred at (gu) : 90.90271 88.96811 87.41505 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4235 nv = 96 ne = 84 npr = 57062 no. pairs analyzed = 57062 no. exposed pairs = 3945 no. arc points = 27707 no. surface atoms = 1328 nbur = 1038 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 152 mr = 1825 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2433 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5493 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6131625E-08 -1.2568504E-08 midg,1,midg; midg,igrid,midg -3.0059070E-08 -1.9046901E-08 1,midg,midg; igrid,midg,midg -1.9423524E-08 -2.9462829E-08 gauss-seidel spectral radius is 0.9847072 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 14:29:50 rms-change max change #iterations 0.1238532 23.54634 at 10iterations 2.6693620E-02 6.801941 at 20iterations 8.5544027E-03 2.115234 at 30iterations 2.7068900E-03 0.6590881 at 40iterations 8.4798463E-04 0.2069092 at 50iterations finished qdiffx linear iterations at : 14:29:56 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.4798463E-04 0.2069092 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:29:56 3.545u 0.199s 0:06.83 54.6% 0+0k 0+0io 6pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Mar 2 2012 at 14:29:56 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: ILE 3 has a net charge of -0.2480 !!! WARNING: MET 4 has a net charge of -0.2480 !!! WARNING: GLY 5 has a net charge of -0.2480 !!! WARNING: SER 6 has a net charge of -0.5580 !!! WARNING: SER 7 has a net charge of -0.5580 !!! WARNING: VAL 8 has a net charge of -0.2480 !!! WARNING: TYR 9 has a net charge of -0.5870 !!! WARNING: ILE 10 has a net charge of -0.2480 !!! WARNING: THR 11 has a net charge of -0.5580 !!! WARNING: VAL 12 has a net charge of -0.2480 !!! WARNING: GLU 13 has a net charge of -1.2480 !!! WARNING: LEU 14 has a net charge of -0.2480 !!! WARNING: ALA 15 has a net charge of -0.2480 !!! WARNING: ILE 16 has a net charge of -0.2480 !!! WARNING: ALA 17 has a net charge of -0.2480 !!! WARNING: VAL 18 has a net charge of -0.2480 !!! WARNING: LEU 19 has a net charge of -0.2480 !!! WARNING: ALA 20 has a net charge of -0.2480 !!! WARNING: ILE 21 has a net charge of -0.2480 !!! WARNING: LEU 22 has a net charge of -0.2480 !!! WARNING: GLY 23 has a net charge of -0.2480 !!! WARNING: ASN 24 has a net charge of -0.9360 !!! WARNING: VAL 25 has a net charge of -0.2480 !!! WARNING: LEU 26 has a net charge of -0.2480 !!! WARNING: VAL 27 has a net charge of -0.2480 !!! WARNING: CYS 28 has a net charge of -0.3830 !!! WARNING: TRP 29 has a net charge of -0.5420 !!! WARNING: ALA 30 has a net charge of -0.2480 !!! WARNING: VAL 31 has a net charge of -0.2480 !!! WARNING: TRP 32 has a net charge of -0.5420 !!! WARNING: LEU 33 has a net charge of -0.2480 !!! WARNING: ASN 34 has a net charge of -0.9360 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: ASN 36 has a net charge of -0.9360 !!! WARNING: LEU 37 has a net charge of -0.2480 !!! WARNING: GLN 38 has a net charge of -0.9360 !!! WARNING: ASN 39 has a net charge of -0.9360 !!! WARNING: VAL 40 has a net charge of -0.2480 !!! WARNING: THR 41 has a net charge of -0.5580 !!! WARNING: ASN 42 has a net charge of -0.9360 !!! WARNING: TYR 43 has a net charge of -0.5870 !!! WARNING: PHE 44 has a net charge of -0.2480 !!! WARNING: VAL 45 has a net charge of -0.2480 !!! WARNING: VAL 46 has a net charge of -0.2480 !!! WARNING: SER 47 has a net charge of -0.5580 !!! WARNING: LEU 48 has a net charge of -0.2480 !!! WARNING: ALA 49 has a net charge of -0.2480 !!! WARNING: ALA 50 has a net charge of -0.2480 !!! WARNING: ALA 51 has a net charge of -0.2480 !!! WARNING: ASP 52 has a net charge of -1.2480 !!! WARNING: ILE 53 has a net charge of -0.2480 !!! WARNING: ALA 54 has a net charge of -0.2480 !!! WARNING: VAL 55 has a net charge of -0.2480 !!! WARNING: GLY 56 has a net charge of -0.2480 !!! WARNING: VAL 57 has a net charge of -0.2480 !!! WARNING: LEU 58 has a net charge of -0.2480 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: ILE 60 has a net charge of -0.2480 !!! WARNING: PHE 62 has a net charge of -0.2480 !!! WARNING: ALA 63 has a net charge of -0.2480 !!! WARNING: ILE 64 has a net charge of -0.2480 !!! WARNING: THR 65 has a net charge of -0.5580 !!! WARNING: ILE 66 has a net charge of -0.2480 !!! WARNING: SER 67 has a net charge of -0.5580 !!! WARNING: THR 68 has a net charge of -0.5580 !!! WARNING: GLY 69 has a net charge of -0.2480 !!! WARNING: PHE 70 has a net charge of -0.2480 !!! WARNING: CYX 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: ALA 73 has a net charge of -0.2480 !!! WARNING: CYX 74 has a net charge of -0.2480 !!! WARNING: HIE 75 has a net charge of -0.5680 !!! WARNING: GLY 76 has a net charge of -0.2480 !!! WARNING: CYX 77 has a net charge of -0.2480 !!! WARNING: LEU 78 has a net charge of -0.2480 !!! WARNING: PHE 79 has a net charge of -0.2480 !!! WARNING: ILE 80 has a net charge of -0.2480 !!! WARNING: ALA 81 has a net charge of -0.2480 !!! WARNING: CYS 82 has a net charge of -0.3830 !!! WARNING: PHE 83 has a net charge of -0.2480 !!! WARNING: VAL 84 has a net charge of -0.2480 !!! WARNING: LEU 85 has a net charge of -0.2480 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: LEU 87 has a net charge of -0.2480 !!! WARNING: THR 88 has a net charge of -0.5580 !!! WARNING: GLN 89 has a net charge of -0.9360 !!! WARNING: SER 90 has a net charge of -0.5580 !!! WARNING: SER 91 has a net charge of -0.5580 !!! WARNING: ILE 92 has a net charge of -0.2480 !!! WARNING: PHE 93 has a net charge of -0.2480 !!! WARNING: SER 94 has a net charge of -0.5580 !!! WARNING: LEU 95 has a net charge of -0.2480 !!! WARNING: LEU 96 has a net charge of -0.2480 !!! WARNING: ALA 97 has a net charge of -0.2480 !!! WARNING: ILE 98 has a net charge of -0.2480 !!! WARNING: ALA 99 has a net charge of -0.2480 !!! WARNING: ILE 100 has a net charge of -0.2480 !!! WARNING: ASP 101 has a net charge of -1.2480 !!! WARNING: ARG 102 has a net charge of -0.9880 !!! WARNING: TYR 103 has a net charge of -0.5870 !!! WARNING: ILE 104 has a net charge of -0.2480 !!! WARNING: ALA 105 has a net charge of -0.2480 !!! WARNING: ILE 106 has a net charge of -0.2480 !!! WARNING: ARG 107 has a net charge of -0.9880 !!! WARNING: ILE 108 has a net charge of -0.2480 !!! WARNING: LEU 110 has a net charge of -0.2480 !!! WARNING: ARG 111 has a net charge of -0.9880 !!! WARNING: TYR 112 has a net charge of -0.5870 !!! WARNING: ASN 113 has a net charge of -0.9360 !!! WARNING: GLY 114 has a net charge of -0.2480 !!! WARNING: LEU 115 has a net charge of -0.2480 !!! WARNING: VAL 116 has a net charge of -0.2480 !!! WARNING: THR 117 has a net charge of -0.5580 !!! WARNING: GLY 118 has a net charge of -0.2480 !!! WARNING: THR 119 has a net charge of -0.5580 !!! WARNING: ARG 120 has a net charge of -0.9880 !!! WARNING: ALA 121 has a net charge of -0.2480 !!! WARNING: LYS 122 has a net charge of -0.1810 !!! WARNING: GLY 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: ILE 125 has a net charge of -0.2480 !!! WARNING: ALA 126 has a net charge of -0.2480 !!! WARNING: ILE 127 has a net charge of -0.2480 !!! WARNING: CYS 128 has a net charge of -0.3830 !!! WARNING: TRP 129 has a net charge of -0.5420 !!! WARNING: VAL 130 has a net charge of -0.2480 !!! WARNING: LEU 131 has a net charge of -0.2480 !!! WARNING: SER 132 has a net charge of -0.5580 !!! WARNING: PHE 133 has a net charge of -0.2480 !!! WARNING: ALA 134 has a net charge of -0.2480 !!! WARNING: ILE 135 has a net charge of -0.2480 !!! WARNING: GLY 136 has a net charge of -0.2480 !!! WARNING: LEU 137 has a net charge of -0.2480 !!! WARNING: THR 138 has a net charge of -0.5580 !!! WARNING: MET 140 has a net charge of -0.2480 !!! WARNING: LEU 141 has a net charge of -0.2480 !!! WARNING: GLY 142 has a net charge of -0.2480 !!! WARNING: TRP 143 has a net charge of -0.5420 !!! WARNING: ASN 144 has a net charge of -0.9360 !!! WARNING: ASN 145 has a net charge of -0.9360 !!! WARNING: CYX 146 has a net charge of -0.2480 !!! WARNING: GLY 147 has a net charge of -0.2480 !!! WARNING: GLN 148 has a net charge of -0.9360 !!! WARNING: SER 156 has a net charge of -0.5580 !!! WARNING: GLN 157 has a net charge of -0.9360 !!! WARNING: GLY 158 has a net charge of -0.2480 !!! WARNING: CYX 159 has a net charge of -0.2480 !!! WARNING: GLY 160 has a net charge of -0.2480 !!! WARNING: GLU 161 has a net charge of -1.2480 !!! WARNING: GLY 162 has a net charge of -0.2480 !!! WARNING: GLN 163 has a net charge of -0.9360 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: ALA 165 has a net charge of -0.2480 !!! WARNING: CYX 166 has a net charge of -0.2480 !!! WARNING: LEU 167 has a net charge of -0.2480 !!! WARNING: PHE 168 has a net charge of -0.2480 !!! WARNING: GLU 169 has a net charge of -1.2480 !!! WARNING: ASP 170 has a net charge of -1.2480 !!! WARNING: VAL 171 has a net charge of -0.2480 !!! WARNING: VAL 172 has a net charge of -0.2480 !!! WARNING: MET 174 has a net charge of -0.2480 !!! WARNING: ASN 175 has a net charge of -0.9360 !!! WARNING: TYR 176 has a net charge of -0.5870 !!! WARNING: MET 177 has a net charge of -0.2480 !!! WARNING: VAL 178 has a net charge of -0.2480 !!! WARNING: TYR 179 has a net charge of -0.5870 !!! WARNING: PHE 180 has a net charge of -0.2480 !!! WARNING: ASN 181 has a net charge of -0.9360 !!! WARNING: PHE 182 has a net charge of -0.2480 !!! WARNING: PHE 183 has a net charge of -0.2480 !!! WARNING: ALA 184 has a net charge of -0.2480 !!! WARNING: CYS 185 has a net charge of -0.3830 !!! WARNING: VAL 186 has a net charge of -0.2480 !!! WARNING: LEU 187 has a net charge of -0.2480 !!! WARNING: VAL 188 has a net charge of -0.2480 !!! WARNING: LEU 190 has a net charge of -0.2480 !!! WARNING: LEU 191 has a net charge of -0.2480 !!! WARNING: LEU 192 has a net charge of -0.2480 !!! WARNING: MET 193 has a net charge of -0.2480 !!! WARNING: LEU 194 has a net charge of -0.2480 !!! WARNING: GLY 195 has a net charge of -0.2480 !!! WARNING: VAL 196 has a net charge of -0.2480 !!! WARNING: TYR 197 has a net charge of -0.5870 !!! WARNING: LEU 198 has a net charge of -0.2480 !!! WARNING: ARG 199 has a net charge of -0.9880 !!! WARNING: ILE 200 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: LEU 202 has a net charge of -0.2480 !!! WARNING: ALA 203 has a net charge of -0.2480 !!! WARNING: ALA 204 has a net charge of -0.2480 !!! WARNING: ARG 205 has a net charge of -0.9880 !!! WARNING: ARG 206 has a net charge of -0.9880 !!! WARNING: GLN 207 has a net charge of -0.9360 !!! WARNING: LEU 208 has a net charge of -0.2480 !!! WARNING: ARG 222 has a net charge of -0.9880 !!! WARNING: SER 223 has a net charge of -0.5580 !!! WARNING: THR 224 has a net charge of -0.5580 !!! WARNING: LEU 225 has a net charge of -0.2480 !!! WARNING: GLN 226 has a net charge of -0.9360 !!! WARNING: LYS 227 has a net charge of -0.1810 !!! WARNING: GLU 228 has a net charge of -1.2480 !!! WARNING: VAL 229 has a net charge of -0.2480 !!! WARNING: HIE 230 has a net charge of -0.5680 !!! WARNING: ALA 231 has a net charge of -0.2480 !!! WARNING: ALA 232 has a net charge of -0.2480 !!! WARNING: LYS 233 has a net charge of -0.1810 !!! WARNING: SER 234 has a net charge of -0.5580 !!! WARNING: LEU 235 has a net charge of -0.2480 !!! WARNING: ALA 236 has a net charge of -0.2480 !!! WARNING: ILE 237 has a net charge of -0.2480 !!! WARNING: ILE 238 has a net charge of -0.2480 !!! WARNING: VAL 239 has a net charge of -0.2480 !!! WARNING: GLY 240 has a net charge of -0.2480 !!! WARNING: LEU 241 has a net charge of -0.2480 !!! WARNING: PHE 242 has a net charge of -0.2480 !!! WARNING: ALA 243 has a net charge of -0.2480 !!! WARNING: LEU 244 has a net charge of -0.2480 !!! WARNING: CYS 245 has a net charge of -0.3830 !!! WARNING: TRP 246 has a net charge of -0.5420 !!! WARNING: LEU 247 has a net charge of -0.2480 !!! WARNING: LEU 249 has a net charge of -0.2480 !!! WARNING: HIE 250 has a net charge of -0.5680 !!! WARNING: ILE 251 has a net charge of -0.2480 !!! WARNING: ILE 252 has a net charge of -0.2480 !!! WARNING: ASN 253 has a net charge of -0.9360 !!! WARNING: CYS 254 has a net charge of -0.3830 !!! WARNING: PHE 255 has a net charge of -0.2480 !!! WARNING: THR 256 has a net charge of -0.5580 !!! WARNING: PHE 257 has a net charge of -0.2480 !!! WARNING: PHE 258 has a net charge of -0.2480 !!! WARNING: CYX 259 has a net charge of -0.2480 !!! WARNING: ASP 261 has a net charge of -1.2480 !!! WARNING: CYX 262 has a net charge of -0.2480 !!! WARNING: SER 263 has a net charge of -0.5580 !!! WARNING: HIP 264 has a net charge of -0.2120 !!! WARNING: ALA 265 has a net charge of -0.2480 !!! WARNING: LEU 267 has a net charge of -0.2480 !!! WARNING: TRP 268 has a net charge of -0.5420 !!! WARNING: LEU 269 has a net charge of -0.2480 !!! WARNING: MET 270 has a net charge of -0.2480 !!! WARNING: TYR 271 has a net charge of -0.5870 !!! WARNING: LEU 272 has a net charge of -0.2480 !!! WARNING: ALA 273 has a net charge of -0.2480 !!! WARNING: ILE 274 has a net charge of -0.2480 !!! WARNING: VAL 275 has a net charge of -0.2480 !!! WARNING: LEU 276 has a net charge of -0.2480 !!! WARNING: SER 277 has a net charge of -0.5580 !!! WARNING: THR 279 has a net charge of -0.5580 !!! WARNING: ASN 280 has a net charge of -0.9360 !!! WARNING: SER 281 has a net charge of -0.5580 !!! WARNING: VAL 282 has a net charge of -0.2480 !!! WARNING: VAL 283 has a net charge of -0.2480 !!! WARNING: ASN 284 has a net charge of -0.9360 !!! WARNING: PHE 286 has a net charge of -0.2480 !!! WARNING: ILE 287 has a net charge of -0.2480 !!! WARNING: TYR 288 has a net charge of -0.5870 !!! WARNING: ALA 289 has a net charge of -0.2480 !!! WARNING: TYR 290 has a net charge of -0.5870 !!! WARNING: ARG 291 has a net charge of -0.9880 !!! WARNING: ILE 292 has a net charge of -0.2480 !!! WARNING: ARG 293 has a net charge of -0.9880 !!! WARNING: GLU 294 has a net charge of -1.2480 !!! WARNING: PHE 295 has a net charge of -0.2480 !!! WARNING: ARG 296 has a net charge of -0.9880 !!! WARNING: GLN 297 has a net charge of -0.9360 !!! WARNING: THR 298 has a net charge of -0.5580 !!! WARNING: PHE 299 has a net charge of -0.2480 !!! WARNING: ARG 300 has a net charge of -0.9880 !!! WARNING: LYS 301 has a net charge of -0.1810 !!! WARNING: ILE 302 has a net charge of -0.2480 !!! WARNING: ILE 303 has a net charge of -0.2480 !!! WARNING: ARG 304 has a net charge of -0.9880 !!! WARNING: SER 305 has a net charge of -0.5580 !!! WARNING: HIE 306 has a net charge of -0.5680 !!! WARNING: VAL 307 has a net charge of -0.2480 !!! WARNING: LEU 308 has a net charge of -0.2480 !!! WARNING: ARG 309 has a net charge of -0.9880 !!! WARNING: GLN 310 has a net charge of -0.9360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.452607 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -32.54400 15.91000 ymin,ymax (A): -36.44200 24.72600 zmin,zma (A): 6.767000 80.29000 x,y,z range (A): 48.45400 61.16800 73.52300 scale (grids/A): 1.452607 object centre (A): -8.316999 -5.858001 43.52850 number of atom coordinates read : 2366 total number of charged atoms : 2235 net assigned charge : -119.1277 assigned positive charge : 275.7153 centred at (gu) : 92.68068 86.87885 82.63023 assigned negative charge : -394.8429 centred at (gu) : 92.70810 86.90448 82.24518 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27707 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 12281 mr = 29284 m= 956 mr = 7338 m= 10 mr = 297 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2500000 number of dielectric boundary points 23889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 16977 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.4842022 object centre at (A) : -8.316999 -5.858001 43.52850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3467789 -0.1164245 midg,1,midg; midg,igrid,midg -6.9850810E-02 -4.4900689E-02 1,midg,midg; igrid,midg,midg -4.0306754E-02 -6.7603908E-02 gauss-seidel spectral radius is 0.9982625 estimated iterations to convergence 190 setup time was (sec) 0.4900000 now iterating at: 14:29:57 rms-change max change #iterations 2.947287 195.2468 at 10iterations 1.239474 60.71834 at 20iterations 0.5433843 25.69940 at 30iterations 0.2415071 11.66226 at 40iterations 0.1143133 6.158783 at 50iterations 5.4696653E-02 2.995682 at 60iterations 3.2182962E-02 2.009521 at 70iterations 2.0664576E-02 1.039063 at 80iterations 1.3416958E-02 0.6986389 at 90iterations 9.2276921E-03 0.4523315 at 100iterations 6.4220126E-03 0.3128662 at 110iterations 4.4557545E-03 0.2155457 at 120iterations finished qdiffx linear iterations at : 14:30:06 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 4.4557545E-03 0.2155457 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 14:30:07 8.529u 0.224s 0:10.55 82.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Fri Mar 2 2012 at 14:30:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: ILE 3 has a net charge of -0.2480 !!! WARNING: MET 4 has a net charge of -0.2480 !!! WARNING: GLY 5 has a net charge of -0.2480 !!! WARNING: SER 6 has a net charge of -0.5580 !!! WARNING: SER 7 has a net charge of -0.5580 !!! WARNING: VAL 8 has a net charge of -0.2480 !!! WARNING: TYR 9 has a net charge of -0.5870 !!! WARNING: ILE 10 has a net charge of -0.2480 !!! WARNING: THR 11 has a net charge of -0.5580 !!! WARNING: VAL 12 has a net charge of -0.2480 !!! WARNING: GLU 13 has a net charge of -1.2480 !!! WARNING: LEU 14 has a net charge of -0.2480 !!! WARNING: ALA 15 has a net charge of -0.2480 !!! WARNING: ILE 16 has a net charge of -0.2480 !!! WARNING: ALA 17 has a net charge of -0.2480 !!! WARNING: VAL 18 has a net charge of -0.2480 !!! WARNING: LEU 19 has a net charge of -0.2480 !!! WARNING: ALA 20 has a net charge of -0.2480 !!! WARNING: ILE 21 has a net charge of -0.2480 !!! WARNING: LEU 22 has a net charge of -0.2480 !!! WARNING: GLY 23 has a net charge of -0.2480 !!! WARNING: ASN 24 has a net charge of -0.9360 !!! WARNING: VAL 25 has a net charge of -0.2480 !!! WARNING: LEU 26 has a net charge of -0.2480 !!! WARNING: VAL 27 has a net charge of -0.2480 !!! WARNING: CYS 28 has a net charge of -0.3830 !!! WARNING: TRP 29 has a net charge of -0.5420 !!! WARNING: ALA 30 has a net charge of -0.2480 !!! WARNING: VAL 31 has a net charge of -0.2480 !!! WARNING: TRP 32 has a net charge of -0.5420 !!! WARNING: LEU 33 has a net charge of -0.2480 !!! WARNING: ASN 34 has a net charge of -0.9360 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: ASN 36 has a net charge of -0.9360 !!! WARNING: LEU 37 has a net charge of -0.2480 !!! WARNING: GLN 38 has a net charge of -0.9360 !!! WARNING: ASN 39 has a net charge of -0.9360 !!! WARNING: VAL 40 has a net charge of -0.2480 !!! WARNING: THR 41 has a net charge of -0.5580 !!! WARNING: ASN 42 has a net charge of -0.9360 !!! WARNING: TYR 43 has a net charge of -0.5870 !!! WARNING: PHE 44 has a net charge of -0.2480 !!! WARNING: VAL 45 has a net charge of -0.2480 !!! WARNING: VAL 46 has a net charge of -0.2480 !!! WARNING: SER 47 has a net charge of -0.5580 !!! WARNING: LEU 48 has a net charge of -0.2480 !!! WARNING: ALA 49 has a net charge of -0.2480 !!! WARNING: ALA 50 has a net charge of -0.2480 !!! WARNING: ALA 51 has a net charge of -0.2480 !!! WARNING: ASP 52 has a net charge of -1.2480 !!! WARNING: ILE 53 has a net charge of -0.2480 !!! WARNING: ALA 54 has a net charge of -0.2480 !!! WARNING: VAL 55 has a net charge of -0.2480 !!! WARNING: GLY 56 has a net charge of -0.2480 !!! WARNING: VAL 57 has a net charge of -0.2480 !!! WARNING: LEU 58 has a net charge of -0.2480 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: ILE 60 has a net charge of -0.2480 !!! WARNING: PHE 62 has a net charge of -0.2480 !!! WARNING: ALA 63 has a net charge of -0.2480 !!! WARNING: ILE 64 has a net charge of -0.2480 !!! WARNING: THR 65 has a net charge of -0.5580 !!! WARNING: ILE 66 has a net charge of -0.2480 !!! WARNING: SER 67 has a net charge of -0.5580 !!! WARNING: THR 68 has a net charge of -0.5580 !!! WARNING: GLY 69 has a net charge of -0.2480 !!! WARNING: PHE 70 has a net charge of -0.2480 !!! WARNING: CYX 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: ALA 73 has a net charge of -0.2480 !!! WARNING: CYX 74 has a net charge of -0.2480 !!! WARNING: HIE 75 has a net charge of -0.5680 !!! WARNING: GLY 76 has a net charge of -0.2480 !!! WARNING: CYX 77 has a net charge of -0.2480 !!! WARNING: LEU 78 has a net charge of -0.2480 !!! WARNING: PHE 79 has a net charge of -0.2480 !!! WARNING: ILE 80 has a net charge of -0.2480 !!! WARNING: ALA 81 has a net charge of -0.2480 !!! WARNING: CYS 82 has a net charge of -0.3830 !!! WARNING: PHE 83 has a net charge of -0.2480 !!! WARNING: VAL 84 has a net charge of -0.2480 !!! WARNING: LEU 85 has a net charge of -0.2480 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: LEU 87 has a net charge of -0.2480 !!! WARNING: THR 88 has a net charge of -0.5580 !!! WARNING: GLN 89 has a net charge of -0.9360 !!! WARNING: SER 90 has a net charge of -0.5580 !!! WARNING: SER 91 has a net charge of -0.5580 !!! WARNING: ILE 92 has a net charge of -0.2480 !!! WARNING: PHE 93 has a net charge of -0.2480 !!! WARNING: SER 94 has a net charge of -0.5580 !!! WARNING: LEU 95 has a net charge of -0.2480 !!! WARNING: LEU 96 has a net charge of -0.2480 !!! WARNING: ALA 97 has a net charge of -0.2480 !!! WARNING: ILE 98 has a net charge of -0.2480 !!! WARNING: ALA 99 has a net charge of -0.2480 !!! WARNING: ILE 100 has a net charge of -0.2480 !!! WARNING: ASP 101 has a net charge of -1.2480 !!! WARNING: ARG 102 has a net charge of -0.9880 !!! WARNING: TYR 103 has a net charge of -0.5870 !!! WARNING: ILE 104 has a net charge of -0.2480 !!! WARNING: ALA 105 has a net charge of -0.2480 !!! WARNING: ILE 106 has a net charge of -0.2480 !!! WARNING: ARG 107 has a net charge of -0.9880 !!! WARNING: ILE 108 has a net charge of -0.2480 !!! WARNING: LEU 110 has a net charge of -0.2480 !!! WARNING: ARG 111 has a net charge of -0.9880 !!! WARNING: TYR 112 has a net charge of -0.5870 !!! WARNING: ASN 113 has a net charge of -0.9360 !!! WARNING: GLY 114 has a net charge of -0.2480 !!! WARNING: LEU 115 has a net charge of -0.2480 !!! WARNING: VAL 116 has a net charge of -0.2480 !!! WARNING: THR 117 has a net charge of -0.5580 !!! WARNING: GLY 118 has a net charge of -0.2480 !!! WARNING: THR 119 has a net charge of -0.5580 !!! WARNING: ARG 120 has a net charge of -0.9880 !!! WARNING: ALA 121 has a net charge of -0.2480 !!! WARNING: LYS 122 has a net charge of -0.1810 !!! WARNING: GLY 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: ILE 125 has a net charge of -0.2480 !!! WARNING: ALA 126 has a net charge of -0.2480 !!! WARNING: ILE 127 has a net charge of -0.2480 !!! WARNING: CYS 128 has a net charge of -0.3830 !!! WARNING: TRP 129 has a net charge of -0.5420 !!! WARNING: VAL 130 has a net charge of -0.2480 !!! WARNING: LEU 131 has a net charge of -0.2480 !!! WARNING: SER 132 has a net charge of -0.5580 !!! WARNING: PHE 133 has a net charge of -0.2480 !!! WARNING: ALA 134 has a net charge of -0.2480 !!! WARNING: ILE 135 has a net charge of -0.2480 !!! WARNING: GLY 136 has a net charge of -0.2480 !!! WARNING: LEU 137 has a net charge of -0.2480 !!! WARNING: THR 138 has a net charge of -0.5580 !!! WARNING: MET 140 has a net charge of -0.2480 !!! WARNING: LEU 141 has a net charge of -0.2480 !!! WARNING: GLY 142 has a net charge of -0.2480 !!! WARNING: TRP 143 has a net charge of -0.5420 !!! WARNING: ASN 144 has a net charge of -0.9360 !!! WARNING: ASN 145 has a net charge of -0.9360 !!! WARNING: CYX 146 has a net charge of -0.2480 !!! WARNING: GLY 147 has a net charge of -0.2480 !!! WARNING: GLN 148 has a net charge of -0.9360 !!! WARNING: SER 156 has a net charge of -0.5580 !!! WARNING: GLN 157 has a net charge of -0.9360 !!! WARNING: GLY 158 has a net charge of -0.2480 !!! WARNING: CYX 159 has a net charge of -0.2480 !!! WARNING: GLY 160 has a net charge of -0.2480 !!! WARNING: GLU 161 has a net charge of -1.2480 !!! WARNING: GLY 162 has a net charge of -0.2480 !!! WARNING: GLN 163 has a net charge of -0.9360 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: ALA 165 has a net charge of -0.2480 !!! WARNING: CYX 166 has a net charge of -0.2480 !!! WARNING: LEU 167 has a net charge of -0.2480 !!! WARNING: PHE 168 has a net charge of -0.2480 !!! WARNING: GLU 169 has a net charge of -1.2480 !!! WARNING: ASP 170 has a net charge of -1.2480 !!! WARNING: VAL 171 has a net charge of -0.2480 !!! WARNING: VAL 172 has a net charge of -0.2480 !!! WARNING: MET 174 has a net charge of -0.2480 !!! WARNING: ASN 175 has a net charge of -0.9360 !!! WARNING: TYR 176 has a net charge of -0.5870 !!! WARNING: MET 177 has a net charge of -0.2480 !!! WARNING: VAL 178 has a net charge of -0.2480 !!! WARNING: TYR 179 has a net charge of -0.5870 !!! WARNING: PHE 180 has a net charge of -0.2480 !!! WARNING: ASN 181 has a net charge of -0.9360 !!! WARNING: PHE 182 has a net charge of -0.2480 !!! WARNING: PHE 183 has a net charge of -0.2480 !!! WARNING: ALA 184 has a net charge of -0.2480 !!! WARNING: CYS 185 has a net charge of -0.3830 !!! WARNING: VAL 186 has a net charge of -0.2480 !!! WARNING: LEU 187 has a net charge of -0.2480 !!! WARNING: VAL 188 has a net charge of -0.2480 !!! WARNING: LEU 190 has a net charge of -0.2480 !!! WARNING: LEU 191 has a net charge of -0.2480 !!! WARNING: LEU 192 has a net charge of -0.2480 !!! WARNING: MET 193 has a net charge of -0.2480 !!! WARNING: LEU 194 has a net charge of -0.2480 !!! WARNING: GLY 195 has a net charge of -0.2480 !!! WARNING: VAL 196 has a net charge of -0.2480 !!! WARNING: TYR 197 has a net charge of -0.5870 !!! WARNING: LEU 198 has a net charge of -0.2480 !!! WARNING: ARG 199 has a net charge of -0.9880 !!! WARNING: ILE 200 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: LEU 202 has a net charge of -0.2480 !!! WARNING: ALA 203 has a net charge of -0.2480 !!! WARNING: ALA 204 has a net charge of -0.2480 !!! WARNING: ARG 205 has a net charge of -0.9880 !!! WARNING: ARG 206 has a net charge of -0.9880 !!! WARNING: GLN 207 has a net charge of -0.9360 !!! WARNING: LEU 208 has a net charge of -0.2480 !!! WARNING: ARG 222 has a net charge of -0.9880 !!! WARNING: SER 223 has a net charge of -0.5580 !!! WARNING: THR 224 has a net charge of -0.5580 !!! WARNING: LEU 225 has a net charge of -0.2480 !!! WARNING: GLN 226 has a net charge of -0.9360 !!! WARNING: LYS 227 has a net charge of -0.1810 !!! WARNING: GLU 228 has a net charge of -1.2480 !!! WARNING: VAL 229 has a net charge of -0.2480 !!! WARNING: HIE 230 has a net charge of -0.5680 !!! WARNING: ALA 231 has a net charge of -0.2480 !!! WARNING: ALA 232 has a net charge of -0.2480 !!! WARNING: LYS 233 has a net charge of -0.1810 !!! WARNING: SER 234 has a net charge of -0.5580 !!! WARNING: LEU 235 has a net charge of -0.2480 !!! WARNING: ALA 236 has a net charge of -0.2480 !!! WARNING: ILE 237 has a net charge of -0.2480 !!! WARNING: ILE 238 has a net charge of -0.2480 !!! WARNING: VAL 239 has a net charge of -0.2480 !!! WARNING: GLY 240 has a net charge of -0.2480 !!! WARNING: LEU 241 has a net charge of -0.2480 !!! WARNING: PHE 242 has a net charge of -0.2480 !!! WARNING: ALA 243 has a net charge of -0.2480 !!! WARNING: LEU 244 has a net charge of -0.2480 !!! WARNING: CYS 245 has a net charge of -0.3830 !!! WARNING: TRP 246 has a net charge of -0.5420 !!! WARNING: LEU 247 has a net charge of -0.2480 !!! WARNING: LEU 249 has a net charge of -0.2480 !!! WARNING: HIE 250 has a net charge of -0.5680 !!! WARNING: ILE 251 has a net charge of -0.2480 !!! WARNING: ILE 252 has a net charge of -0.2480 !!! WARNING: ASN 253 has a net charge of -0.9360 !!! WARNING: CYS 254 has a net charge of -0.3830 !!! WARNING: PHE 255 has a net charge of -0.2480 !!! WARNING: THR 256 has a net charge of -0.5580 !!! WARNING: PHE 257 has a net charge of -0.2480 !!! WARNING: PHE 258 has a net charge of -0.2480 !!! WARNING: CYX 259 has a net charge of -0.2480 !!! WARNING: ASP 261 has a net charge of -1.2480 !!! WARNING: CYX 262 has a net charge of -0.2480 !!! WARNING: SER 263 has a net charge of -0.5580 !!! WARNING: HIP 264 has a net charge of -0.2120 !!! WARNING: ALA 265 has a net charge of -0.2480 !!! WARNING: LEU 267 has a net charge of -0.2480 !!! WARNING: TRP 268 has a net charge of -0.5420 !!! WARNING: LEU 269 has a net charge of -0.2480 !!! WARNING: MET 270 has a net charge of -0.2480 !!! WARNING: TYR 271 has a net charge of -0.5870 !!! WARNING: LEU 272 has a net charge of -0.2480 !!! WARNING: ALA 273 has a net charge of -0.2480 !!! WARNING: ILE 274 has a net charge of -0.2480 !!! WARNING: VAL 275 has a net charge of -0.2480 !!! WARNING: LEU 276 has a net charge of -0.2480 !!! WARNING: SER 277 has a net charge of -0.5580 !!! WARNING: THR 279 has a net charge of -0.5580 !!! WARNING: ASN 280 has a net charge of -0.9360 !!! WARNING: SER 281 has a net charge of -0.5580 !!! WARNING: VAL 282 has a net charge of -0.2480 !!! WARNING: VAL 283 has a net charge of -0.2480 !!! WARNING: ASN 284 has a net charge of -0.9360 !!! WARNING: PHE 286 has a net charge of -0.2480 !!! WARNING: ILE 287 has a net charge of -0.2480 !!! WARNING: TYR 288 has a net charge of -0.5870 !!! WARNING: ALA 289 has a net charge of -0.2480 !!! WARNING: TYR 290 has a net charge of -0.5870 !!! WARNING: ARG 291 has a net charge of -0.9880 !!! WARNING: ILE 292 has a net charge of -0.2480 !!! WARNING: ARG 293 has a net charge of -0.9880 !!! WARNING: GLU 294 has a net charge of -1.2480 !!! WARNING: PHE 295 has a net charge of -0.2480 !!! WARNING: ARG 296 has a net charge of -0.9880 !!! WARNING: GLN 297 has a net charge of -0.9360 !!! WARNING: THR 298 has a net charge of -0.5580 !!! WARNING: PHE 299 has a net charge of -0.2480 !!! WARNING: ARG 300 has a net charge of -0.9880 !!! WARNING: LYS 301 has a net charge of -0.1810 !!! WARNING: ILE 302 has a net charge of -0.2480 !!! WARNING: ILE 303 has a net charge of -0.2480 !!! WARNING: ARG 304 has a net charge of -0.9880 !!! WARNING: SER 305 has a net charge of -0.5580 !!! WARNING: HIE 306 has a net charge of -0.5680 !!! WARNING: VAL 307 has a net charge of -0.2480 !!! WARNING: LEU 308 has a net charge of -0.2480 !!! WARNING: ARG 309 has a net charge of -0.9880 !!! WARNING: GLN 310 has a net charge of -0.9360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.178910 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -32.54400 15.91000 ymin,ymax (A): -36.44200 24.72600 zmin,zma (A): 6.767000 80.29000 x,y,z range (A): 48.45400 61.16800 73.52300 scale (grids/A): 2.178910 object centre (A): -8.316999 -5.858001 43.52850 number of atom coordinates read : 2366 total number of charged atoms : 2235 net assigned charge : -119.1277 assigned positive charge : 275.7153 centred at (gu) : 94.02095 85.31823 78.94535 assigned negative charge : -394.8429 centred at (gu) : 94.06211 85.35675 78.36776 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 110817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27707 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 44363 mr = 73332 m= 10500 mr = 32171 m= 1149 mr = 6927 m= 30 mr = 600 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.5900000 number of dielectric boundary points 53827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17879 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.452607 object centre at (A) : -8.316999 -5.858001 43.52850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.538357 -1.422748 midg,1,midg; midg,igrid,midg -0.7464036 -0.4438805 1,midg,midg; igrid,midg,midg -0.4298847 -0.7327837 gauss-seidel spectral radius is 0.9991232 estimated iterations to convergence 267 setup time was (sec) 0.8600000 now iterating at: 14:30:08 rms-change max change #iterations 7.240711 271.8282 at 10iterations 4.044903 124.3284 at 20iterations 2.246878 64.68225 at 30iterations 1.250368 38.28548 at 40iterations 0.6870249 19.38690 at 50iterations 0.3786305 11.42996 at 60iterations 0.2098803 6.272736 at 70iterations 0.1159424 3.517153 at 80iterations 6.4142734E-02 1.947418 at 90iterations 3.6507640E-02 0.9980621 at 100iterations 2.1637382E-02 0.6262207 at 110iterations 1.3550656E-02 0.4668579 at 120iterations 8.9039188E-03 0.2824707 at 130iterations 6.3601006E-03 0.1976929 at 140iterations 4.8342855E-03 0.1403809 at 150iterations 3.7805396E-03 0.1063538 at 160iterations 2.9931043E-03 8.1329346E-02 at 170iterations 2.3983240E-03 6.4666748E-02 at 180iterations finished qdiffx linear iterations at : 14:30:33 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 2.3983240E-03 6.4666748E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.19000 DelPhi exited at 14:30:33 14.194u 0.249s 0:26.57 54.3% 0+0k 0+0io 0pf+0w