Fri Mar 2 14:29:52 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 14:29:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2238 !!! WARNING: TYR 32 has a net charge of -0.5870 !!! WARNING: ALA 33 has a net charge of -0.2480 !!! WARNING: LEU 34 has a net charge of -0.2480 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: TYR 36 has a net charge of -0.5870 !!! WARNING: CYS 37 has a net charge of -0.3830 !!! WARNING: ALA 38 has a net charge of -0.2480 !!! WARNING: LEU 39 has a net charge of -0.2480 !!! WARNING: ILE 40 has a net charge of -0.2480 !!! WARNING: LEU 41 has a net charge of -0.2480 !!! WARNING: ALA 42 has a net charge of -0.2480 !!! WARNING: ILE 43 has a net charge of -0.2480 !!! WARNING: VAL 44 has a net charge of -0.2480 !!! WARNING: PHE 45 has a net charge of -0.2480 !!! WARNING: GLY 46 has a net charge of -0.2480 !!! WARNING: ASN 47 has a net charge of -0.9360 !!! WARNING: GLY 48 has a net charge of -0.2480 !!! WARNING: LEU 49 has a net charge of -0.2480 !!! WARNING: VAL 50 has a net charge of -0.2480 !!! WARNING: CYS 51 has a net charge of -0.3830 !!! WARNING: MET 52 has a net charge of -0.2480 !!! WARNING: ALA 53 has a net charge of -0.2480 !!! WARNING: VAL 54 has a net charge of -0.2480 !!! WARNING: LEU 55 has a net charge of -0.2480 !!! WARNING: LYS 56 has a net charge of -0.1810 !!! WARNING: GLU 57 has a net charge of -1.2480 !!! WARNING: ARG 58 has a net charge of -0.9880 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: LEU 60 has a net charge of -0.2480 !!! WARNING: GLN 61 has a net charge of -0.9360 !!! WARNING: THR 62 has a net charge of -0.5580 !!! WARNING: THR 63 has a net charge of -0.5580 !!! WARNING: THR 64 has a net charge of -0.5580 !!! WARNING: ASN 65 has a net charge of -0.9360 !!! WARNING: TYR 66 has a net charge of -0.5870 !!! WARNING: LEU 67 has a net charge of -0.2480 !!! WARNING: VAL 68 has a net charge of -0.2480 !!! WARNING: VAL 69 has a net charge of -0.2480 !!! WARNING: SER 70 has a net charge of -0.5580 !!! WARNING: LEU 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: VAL 73 has a net charge of -0.2480 !!! WARNING: ALA 74 has a net charge of -0.2480 !!! WARNING: ASP 75 has a net charge of -1.2480 !!! WARNING: LEU 76 has a net charge of -0.2480 !!! WARNING: LEU 77 has a net charge of -0.2480 !!! WARNING: VAL 78 has a net charge of -0.2480 !!! WARNING: ALA 79 has a net charge of -0.2480 !!! WARNING: THR 80 has a net charge of -0.5580 !!! WARNING: LEU 81 has a net charge of -0.2480 !!! WARNING: VAL 82 has a net charge of -0.2480 !!! WARNING: MET 83 has a net charge of -0.2480 !!! WARNING: TRP 85 has a net charge of -0.5420 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: VAL 87 has a net charge of -0.2480 !!! WARNING: TYR 88 has a net charge of -0.5870 !!! WARNING: LEU 89 has a net charge of -0.2480 !!! WARNING: GLU 90 has a net charge of -1.2480 !!! WARNING: VAL 91 has a net charge of -0.2480 !!! WARNING: THR 92 has a net charge of -0.5580 !!! WARNING: GLY 93 has a net charge of -0.2480 !!! WARNING: GLY 94 has a net charge of -0.2480 !!! WARNING: VAL 95 has a net charge of -0.2480 !!! WARNING: TRP 96 has a net charge of -0.5420 !!! WARNING: ASN 97 has a net charge of -0.9360 !!! WARNING: PHE 98 has a net charge of -0.2480 !!! WARNING: SER 99 has a net charge of -0.5580 !!! WARNING: ARG 100 has a net charge of -0.9880 !!! WARNING: ILE 101 has a net charge of -0.2480 !!! WARNING: CYS 102 has a net charge of -0.3830 !!! WARNING: CYX 103 has a net charge of -0.2480 !!! WARNING: ASP 104 has a net charge of -1.2480 !!! WARNING: VAL 105 has a net charge of -0.2480 !!! WARNING: PHE 106 has a net charge of -0.2480 !!! WARNING: VAL 107 has a net charge of -0.2480 !!! WARNING: THR 108 has a net charge of -0.5580 !!! WARNING: LEU 109 has a net charge of -0.2480 !!! WARNING: ASP 110 has a net charge of -1.2480 !!! WARNING: VAL 111 has a net charge of -0.2480 !!! WARNING: MET 112 has a net charge of -0.2480 !!! WARNING: MET 113 has a net charge of -0.2480 !!! WARNING: CYS 114 has a net charge of -0.3830 !!! WARNING: THR 115 has a net charge of -0.5580 !!! WARNING: ALA 116 has a net charge of -0.2480 !!! WARNING: SER 117 has a net charge of -0.5580 !!! WARNING: ILE 118 has a net charge of -0.2480 !!! WARNING: TRP 119 has a net charge of -0.5420 !!! WARNING: ASN 120 has a net charge of -0.9360 !!! WARNING: LEU 121 has a net charge of -0.2480 !!! WARNING: CYS 122 has a net charge of -0.3830 !!! WARNING: ALA 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: SER 125 has a net charge of -0.5580 !!! WARNING: ILE 126 has a net charge of -0.2480 !!! WARNING: ASP 127 has a net charge of -1.2480 !!! WARNING: ARG 128 has a net charge of -0.9880 !!! WARNING: TYR 129 has a net charge of -0.5870 !!! WARNING: THR 130 has a net charge of -0.5580 !!! WARNING: ALA 131 has a net charge of -0.2480 !!! WARNING: VAL 132 has a net charge of -0.2480 !!! WARNING: VAL 133 has a net charge of -0.2480 !!! WARNING: MET 134 has a net charge of -0.2480 !!! WARNING: VAL 136 has a net charge of -0.2480 !!! WARNING: HID 137 has a net charge of -0.5680 !!! WARNING: TYR 138 has a net charge of -0.5870 !!! WARNING: GLN 139 has a net charge of -0.9360 !!! WARNING: HID 140 has a net charge of -0.5680 !!! WARNING: GLY 141 has a net charge of -0.2480 !!! WARNING: THR 142 has a net charge of -0.5580 !!! WARNING: GLY 143 has a net charge of -0.2480 !!! WARNING: GLN 144 has a net charge of -0.2310 !!! WARNING: SER 145 has a net charge of -0.0080 !!! WARNING: SER 146 has a net charge of -0.5580 !!! WARNING: CYS 147 has a net charge of -0.3830 !!! WARNING: ARG 148 has a net charge of -0.9880 !!! WARNING: ARG 149 has a net charge of -0.9880 !!! WARNING: VAL 150 has a net charge of -0.2480 !!! WARNING: ALA 151 has a net charge of -0.2480 !!! WARNING: LEU 152 has a net charge of -0.2480 !!! WARNING: MET 153 has a net charge of -0.2480 !!! WARNING: ILE 154 has a net charge of -0.2480 !!! WARNING: THR 155 has a net charge of -0.5580 !!! WARNING: ALA 156 has a net charge of -0.2480 !!! WARNING: VAL 157 has a net charge of -0.2480 !!! WARNING: TRP 158 has a net charge of -0.5420 !!! WARNING: VAL 159 has a net charge of -0.2480 !!! WARNING: LEU 160 has a net charge of -0.2480 !!! WARNING: ALA 161 has a net charge of -0.2480 !!! WARNING: PHE 162 has a net charge of -0.2480 !!! WARNING: ALA 163 has a net charge of -0.2480 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: SER 165 has a net charge of -0.5580 !!! WARNING: CYS 166 has a net charge of -0.3830 !!! WARNING: LEU 168 has a net charge of -0.2480 !!! WARNING: LEU 169 has a net charge of -0.2480 !!! WARNING: PHE 170 has a net charge of -0.2480 !!! WARNING: GLY 171 has a net charge of -0.2480 !!! WARNING: PHE 172 has a net charge of -0.2480 !!! WARNING: ASN 173 has a net charge of -0.9360 !!! WARNING: THR 174 has a net charge of -0.5580 !!! WARNING: THR 175 has a net charge of -0.5580 !!! WARNING: GLY 176 has a net charge of -0.2480 !!! WARNING: ASP 177 has a net charge of -1.2480 !!! WARNING: THR 179 has a net charge of -0.5580 !!! WARNING: VAL 180 has a net charge of -0.2480 !!! WARNING: CYX 181 has a net charge of -0.2480 !!! WARNING: SER 182 has a net charge of -0.5580 !!! WARNING: ILE 183 has a net charge of -0.2480 !!! WARNING: SER 184 has a net charge of -0.5580 !!! WARNING: ASN 185 has a net charge of -0.9360 !!! WARNING: ASP 187 has a net charge of -1.2480 !!! WARNING: PHE 188 has a net charge of -0.2480 !!! WARNING: VAL 189 has a net charge of -0.2480 !!! WARNING: ILE 190 has a net charge of -0.2480 !!! WARNING: TYR 191 has a net charge of -0.5870 !!! WARNING: SER 192 has a net charge of -0.5580 !!! WARNING: SER 193 has a net charge of -0.5580 !!! WARNING: VAL 194 has a net charge of -0.2480 !!! WARNING: VAL 195 has a net charge of -0.2480 !!! WARNING: SER 196 has a net charge of -0.5580 !!! WARNING: PHE 197 has a net charge of -0.2480 !!! WARNING: TYR 198 has a net charge of -0.5870 !!! WARNING: LEU 199 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: GLY 202 has a net charge of -0.2480 !!! WARNING: VAL 203 has a net charge of -0.2480 !!! WARNING: THR 204 has a net charge of -0.5580 !!! WARNING: VAL 205 has a net charge of -0.2480 !!! WARNING: LEU 206 has a net charge of -0.2480 !!! WARNING: VAL 207 has a net charge of -0.2480 !!! WARNING: TYR 208 has a net charge of -0.5870 !!! WARNING: ALA 209 has a net charge of -0.2480 !!! WARNING: ARG 210 has a net charge of -0.9880 !!! WARNING: ILE 211 has a net charge of -0.2480 !!! WARNING: TYR 212 has a net charge of -0.5870 !!! WARNING: VAL 213 has a net charge of -0.2480 !!! WARNING: VAL 214 has a net charge of -0.2480 !!! WARNING: LEU 215 has a net charge of -0.2480 !!! WARNING: LYS 216 has a net charge of -0.1810 !!! WARNING: GLN 217 has a net charge of -0.9360 !!! WARNING: ARG 218 has a net charge of -0.9880 !!! WARNING: ARG 219 has a net charge of -0.9880 !!! WARNING: ARG 220 has a net charge of -0.9880 !!! WARNING: LYS 221 has a net charge of -0.1810 !!! WARNING: GLY 319 has a net charge of -0.2480 !!! WARNING: VAL 320 has a net charge of -0.2480 !!! WARNING: LEU 322 has a net charge of -0.2480 !!! WARNING: ARG 323 has a net charge of -0.9880 !!! WARNING: GLU 324 has a net charge of -1.2480 !!! WARNING: LYS 325 has a net charge of -0.1810 !!! WARNING: LYS 326 has a net charge of -0.1810 !!! WARNING: ALA 327 has a net charge of -0.2480 !!! WARNING: THR 328 has a net charge of -0.5580 !!! WARNING: GLN 329 has a net charge of -0.9360 !!! WARNING: MET 330 has a net charge of -0.2480 !!! WARNING: VAL 331 has a net charge of -0.2480 !!! WARNING: ALA 332 has a net charge of -0.2480 !!! WARNING: ILE 333 has a net charge of -0.2480 !!! WARNING: VAL 334 has a net charge of -0.2480 !!! WARNING: LEU 335 has a net charge of -0.2480 !!! WARNING: GLY 336 has a net charge of -0.2480 !!! WARNING: ALA 337 has a net charge of -0.2480 !!! WARNING: PHE 338 has a net charge of -0.2480 !!! WARNING: ILE 339 has a net charge of -0.2480 !!! WARNING: VAL 340 has a net charge of -0.2480 !!! WARNING: CYS 341 has a net charge of -0.3830 !!! WARNING: TRP 342 has a net charge of -0.5420 !!! WARNING: LEU 343 has a net charge of -0.2480 !!! WARNING: PHE 345 has a net charge of -0.2480 !!! WARNING: PHE 346 has a net charge of -0.2480 !!! WARNING: LEU 347 has a net charge of -0.2480 !!! WARNING: THR 348 has a net charge of -0.5580 !!! WARNING: HIE 349 has a net charge of -0.5680 !!! WARNING: VAL 350 has a net charge of -0.2480 !!! WARNING: LEU 351 has a net charge of -0.2480 !!! WARNING: ASN 352 has a net charge of -0.9360 !!! WARNING: THR 353 has a net charge of -0.5580 !!! WARNING: HIE 354 has a net charge of -0.5680 !!! WARNING: CYX 355 has a net charge of -0.2480 !!! WARNING: GLN 356 has a net charge of -0.9360 !!! WARNING: THR 357 has a net charge of -0.0150 !!! WARNING: CYX 358 has a net charge of -0.2480 !!! WARNING: HID 359 has a net charge of -0.5680 !!! WARNING: VAL 360 has a net charge of -0.2480 !!! WARNING: SER 361 has a net charge of -0.5580 !!! WARNING: GLU 363 has a net charge of -1.2480 !!! WARNING: LEU 364 has a net charge of -0.2480 !!! WARNING: TYR 365 has a net charge of -0.5870 !!! WARNING: SER 366 has a net charge of -0.5580 !!! WARNING: ALA 367 has a net charge of -0.2480 !!! WARNING: THR 368 has a net charge of -0.5580 !!! WARNING: THR 369 has a net charge of -0.5580 !!! WARNING: TRP 370 has a net charge of -0.5420 !!! WARNING: LEU 371 has a net charge of -0.2480 !!! WARNING: GLY 372 has a net charge of -0.2480 !!! WARNING: TYR 373 has a net charge of -0.5870 !!! WARNING: VAL 374 has a net charge of -0.2480 !!! WARNING: ASN 375 has a net charge of -0.9360 !!! WARNING: SER 376 has a net charge of -0.5580 !!! WARNING: ALA 377 has a net charge of -0.2480 !!! WARNING: LEU 378 has a net charge of -0.2480 !!! WARNING: ASN 379 has a net charge of -0.9360 !!! WARNING: VAL 381 has a net charge of -0.2480 !!! WARNING: ILE 382 has a net charge of -0.2480 !!! WARNING: TYR 383 has a net charge of -0.5870 !!! WARNING: THR 384 has a net charge of -0.5580 !!! WARNING: THR 385 has a net charge of -0.5580 !!! WARNING: PHE 386 has a net charge of -0.2480 !!! WARNING: ASN 387 has a net charge of -0.9360 !!! WARNING: ILE 388 has a net charge of -0.2480 !!! WARNING: GLU 389 has a net charge of -1.2480 !!! WARNING: PHE 390 has a net charge of -0.2480 !!! WARNING: ARG 391 has a net charge of -0.9880 !!! WARNING: LYS 392 has a net charge of -0.1810 !!! WARNING: ALA 393 has a net charge of -0.2480 !!! WARNING: PHE 394 has a net charge of -0.2480 !!! WARNING: LEU 395 has a net charge of -0.2480 !!! WARNING: LYS 396 has a net charge of -0.1810 !!! WARNING: ILE 397 has a net charge of -0.2480 !!! WARNING: LEU 398 has a net charge of -0.2480 !!! WARNING: SER 399 has a net charge of -0.5580 !!! WARNING: CYS 400 has a net charge of -0.3830 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: 0.5564500 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -11.88000 52.09700 ymin,ymax (A): -14.78700 43.12200 zmin,zma (A): 4.503000 51.66100 x,y,z range (A): 63.97700 57.90900 47.15800 scale (grids/A): 0.5564500 object centre (A): 20.10850 14.16750 28.08200 number of atom coordinates read : 2238 total number of charged atoms : 2107 net assigned charge : -113.9328 assigned positive charge : 259.5184 centred at (gu) : 90.37147 92.40440 90.41981 assigned negative charge : -373.4507 centred at (gu) : 90.32433 92.42525 90.39996 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5497 nv = 96 ne = 84 npr = 54333 no. pairs analyzed = 54333 no. exposed pairs = 3630 no. arc points = 25932 no. surface atoms = 1217 nbur = 1021 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 = 1.540000 m= 272 mr = 2581 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2267 ## 108 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6848760E-09 -1.1447986E-08 midg,1,midg; midg,igrid,midg -5.9260610E-09 -1.9022462E-08 1,midg,midg; igrid,midg,midg -9.9997717E-09 -1.1076229E-08 gauss-seidel spectral radius is 0.9833291 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 14:29:52 rms-change max change #iterations 0.1418555 23.72874 at 10iterations 4.3647990E-02 8.700089 at 20iterations 1.8725926E-02 3.859222 at 30iterations 8.1838733E-03 1.706085 at 40iterations 3.5937652E-03 0.7508240 at 50iterations finished qdiffx linear iterations at : 14:29:58 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 3.5937652E-03 0.7508240 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:29:58 3.569u 0.184s 0:06.51 57.4% 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 14:29:58 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2238 !!! WARNING: TYR 32 has a net charge of -0.5870 !!! WARNING: ALA 33 has a net charge of -0.2480 !!! WARNING: LEU 34 has a net charge of -0.2480 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: TYR 36 has a net charge of -0.5870 !!! WARNING: CYS 37 has a net charge of -0.3830 !!! WARNING: ALA 38 has a net charge of -0.2480 !!! WARNING: LEU 39 has a net charge of -0.2480 !!! WARNING: ILE 40 has a net charge of -0.2480 !!! WARNING: LEU 41 has a net charge of -0.2480 !!! WARNING: ALA 42 has a net charge of -0.2480 !!! WARNING: ILE 43 has a net charge of -0.2480 !!! WARNING: VAL 44 has a net charge of -0.2480 !!! WARNING: PHE 45 has a net charge of -0.2480 !!! WARNING: GLY 46 has a net charge of -0.2480 !!! WARNING: ASN 47 has a net charge of -0.9360 !!! WARNING: GLY 48 has a net charge of -0.2480 !!! WARNING: LEU 49 has a net charge of -0.2480 !!! WARNING: VAL 50 has a net charge of -0.2480 !!! WARNING: CYS 51 has a net charge of -0.3830 !!! WARNING: MET 52 has a net charge of -0.2480 !!! WARNING: ALA 53 has a net charge of -0.2480 !!! WARNING: VAL 54 has a net charge of -0.2480 !!! WARNING: LEU 55 has a net charge of -0.2480 !!! WARNING: LYS 56 has a net charge of -0.1810 !!! WARNING: GLU 57 has a net charge of -1.2480 !!! WARNING: ARG 58 has a net charge of -0.9880 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: LEU 60 has a net charge of -0.2480 !!! WARNING: GLN 61 has a net charge of -0.9360 !!! WARNING: THR 62 has a net charge of -0.5580 !!! WARNING: THR 63 has a net charge of -0.5580 !!! WARNING: THR 64 has a net charge of -0.5580 !!! WARNING: ASN 65 has a net charge of -0.9360 !!! WARNING: TYR 66 has a net charge of -0.5870 !!! WARNING: LEU 67 has a net charge of -0.2480 !!! WARNING: VAL 68 has a net charge of -0.2480 !!! WARNING: VAL 69 has a net charge of -0.2480 !!! WARNING: SER 70 has a net charge of -0.5580 !!! WARNING: LEU 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: VAL 73 has a net charge of -0.2480 !!! WARNING: ALA 74 has a net charge of -0.2480 !!! WARNING: ASP 75 has a net charge of -1.2480 !!! WARNING: LEU 76 has a net charge of -0.2480 !!! WARNING: LEU 77 has a net charge of -0.2480 !!! WARNING: VAL 78 has a net charge of -0.2480 !!! WARNING: ALA 79 has a net charge of -0.2480 !!! WARNING: THR 80 has a net charge of -0.5580 !!! WARNING: LEU 81 has a net charge of -0.2480 !!! WARNING: VAL 82 has a net charge of -0.2480 !!! WARNING: MET 83 has a net charge of -0.2480 !!! WARNING: TRP 85 has a net charge of -0.5420 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: VAL 87 has a net charge of -0.2480 !!! WARNING: TYR 88 has a net charge of -0.5870 !!! WARNING: LEU 89 has a net charge of -0.2480 !!! WARNING: GLU 90 has a net charge of -1.2480 !!! WARNING: VAL 91 has a net charge of -0.2480 !!! WARNING: THR 92 has a net charge of -0.5580 !!! WARNING: GLY 93 has a net charge of -0.2480 !!! WARNING: GLY 94 has a net charge of -0.2480 !!! WARNING: VAL 95 has a net charge of -0.2480 !!! WARNING: TRP 96 has a net charge of -0.5420 !!! WARNING: ASN 97 has a net charge of -0.9360 !!! WARNING: PHE 98 has a net charge of -0.2480 !!! WARNING: SER 99 has a net charge of -0.5580 !!! WARNING: ARG 100 has a net charge of -0.9880 !!! WARNING: ILE 101 has a net charge of -0.2480 !!! WARNING: CYS 102 has a net charge of -0.3830 !!! WARNING: CYX 103 has a net charge of -0.2480 !!! WARNING: ASP 104 has a net charge of -1.2480 !!! WARNING: VAL 105 has a net charge of -0.2480 !!! WARNING: PHE 106 has a net charge of -0.2480 !!! WARNING: VAL 107 has a net charge of -0.2480 !!! WARNING: THR 108 has a net charge of -0.5580 !!! WARNING: LEU 109 has a net charge of -0.2480 !!! WARNING: ASP 110 has a net charge of -1.2480 !!! WARNING: VAL 111 has a net charge of -0.2480 !!! WARNING: MET 112 has a net charge of -0.2480 !!! WARNING: MET 113 has a net charge of -0.2480 !!! WARNING: CYS 114 has a net charge of -0.3830 !!! WARNING: THR 115 has a net charge of -0.5580 !!! WARNING: ALA 116 has a net charge of -0.2480 !!! WARNING: SER 117 has a net charge of -0.5580 !!! WARNING: ILE 118 has a net charge of -0.2480 !!! WARNING: TRP 119 has a net charge of -0.5420 !!! WARNING: ASN 120 has a net charge of -0.9360 !!! WARNING: LEU 121 has a net charge of -0.2480 !!! WARNING: CYS 122 has a net charge of -0.3830 !!! WARNING: ALA 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: SER 125 has a net charge of -0.5580 !!! WARNING: ILE 126 has a net charge of -0.2480 !!! WARNING: ASP 127 has a net charge of -1.2480 !!! WARNING: ARG 128 has a net charge of -0.9880 !!! WARNING: TYR 129 has a net charge of -0.5870 !!! WARNING: THR 130 has a net charge of -0.5580 !!! WARNING: ALA 131 has a net charge of -0.2480 !!! WARNING: VAL 132 has a net charge of -0.2480 !!! WARNING: VAL 133 has a net charge of -0.2480 !!! WARNING: MET 134 has a net charge of -0.2480 !!! WARNING: VAL 136 has a net charge of -0.2480 !!! WARNING: HID 137 has a net charge of -0.5680 !!! WARNING: TYR 138 has a net charge of -0.5870 !!! WARNING: GLN 139 has a net charge of -0.9360 !!! WARNING: HID 140 has a net charge of -0.5680 !!! WARNING: GLY 141 has a net charge of -0.2480 !!! WARNING: THR 142 has a net charge of -0.5580 !!! WARNING: GLY 143 has a net charge of -0.2480 !!! WARNING: GLN 144 has a net charge of -0.2310 !!! WARNING: SER 145 has a net charge of -0.0080 !!! WARNING: SER 146 has a net charge of -0.5580 !!! WARNING: CYS 147 has a net charge of -0.3830 !!! WARNING: ARG 148 has a net charge of -0.9880 !!! WARNING: ARG 149 has a net charge of -0.9880 !!! WARNING: VAL 150 has a net charge of -0.2480 !!! WARNING: ALA 151 has a net charge of -0.2480 !!! WARNING: LEU 152 has a net charge of -0.2480 !!! WARNING: MET 153 has a net charge of -0.2480 !!! WARNING: ILE 154 has a net charge of -0.2480 !!! WARNING: THR 155 has a net charge of -0.5580 !!! WARNING: ALA 156 has a net charge of -0.2480 !!! WARNING: VAL 157 has a net charge of -0.2480 !!! WARNING: TRP 158 has a net charge of -0.5420 !!! WARNING: VAL 159 has a net charge of -0.2480 !!! WARNING: LEU 160 has a net charge of -0.2480 !!! WARNING: ALA 161 has a net charge of -0.2480 !!! WARNING: PHE 162 has a net charge of -0.2480 !!! WARNING: ALA 163 has a net charge of -0.2480 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: SER 165 has a net charge of -0.5580 !!! WARNING: CYS 166 has a net charge of -0.3830 !!! WARNING: LEU 168 has a net charge of -0.2480 !!! WARNING: LEU 169 has a net charge of -0.2480 !!! WARNING: PHE 170 has a net charge of -0.2480 !!! WARNING: GLY 171 has a net charge of -0.2480 !!! WARNING: PHE 172 has a net charge of -0.2480 !!! WARNING: ASN 173 has a net charge of -0.9360 !!! WARNING: THR 174 has a net charge of -0.5580 !!! WARNING: THR 175 has a net charge of -0.5580 !!! WARNING: GLY 176 has a net charge of -0.2480 !!! WARNING: ASP 177 has a net charge of -1.2480 !!! WARNING: THR 179 has a net charge of -0.5580 !!! WARNING: VAL 180 has a net charge of -0.2480 !!! WARNING: CYX 181 has a net charge of -0.2480 !!! WARNING: SER 182 has a net charge of -0.5580 !!! WARNING: ILE 183 has a net charge of -0.2480 !!! WARNING: SER 184 has a net charge of -0.5580 !!! WARNING: ASN 185 has a net charge of -0.9360 !!! WARNING: ASP 187 has a net charge of -1.2480 !!! WARNING: PHE 188 has a net charge of -0.2480 !!! WARNING: VAL 189 has a net charge of -0.2480 !!! WARNING: ILE 190 has a net charge of -0.2480 !!! WARNING: TYR 191 has a net charge of -0.5870 !!! WARNING: SER 192 has a net charge of -0.5580 !!! WARNING: SER 193 has a net charge of -0.5580 !!! WARNING: VAL 194 has a net charge of -0.2480 !!! WARNING: VAL 195 has a net charge of -0.2480 !!! WARNING: SER 196 has a net charge of -0.5580 !!! WARNING: PHE 197 has a net charge of -0.2480 !!! WARNING: TYR 198 has a net charge of -0.5870 !!! WARNING: LEU 199 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: GLY 202 has a net charge of -0.2480 !!! WARNING: VAL 203 has a net charge of -0.2480 !!! WARNING: THR 204 has a net charge of -0.5580 !!! WARNING: VAL 205 has a net charge of -0.2480 !!! WARNING: LEU 206 has a net charge of -0.2480 !!! WARNING: VAL 207 has a net charge of -0.2480 !!! WARNING: TYR 208 has a net charge of -0.5870 !!! WARNING: ALA 209 has a net charge of -0.2480 !!! WARNING: ARG 210 has a net charge of -0.9880 !!! WARNING: ILE 211 has a net charge of -0.2480 !!! WARNING: TYR 212 has a net charge of -0.5870 !!! WARNING: VAL 213 has a net charge of -0.2480 !!! WARNING: VAL 214 has a net charge of -0.2480 !!! WARNING: LEU 215 has a net charge of -0.2480 !!! WARNING: LYS 216 has a net charge of -0.1810 !!! WARNING: GLN 217 has a net charge of -0.9360 !!! WARNING: ARG 218 has a net charge of -0.9880 !!! WARNING: ARG 219 has a net charge of -0.9880 !!! WARNING: ARG 220 has a net charge of -0.9880 !!! WARNING: LYS 221 has a net charge of -0.1810 !!! WARNING: GLY 319 has a net charge of -0.2480 !!! WARNING: VAL 320 has a net charge of -0.2480 !!! WARNING: LEU 322 has a net charge of -0.2480 !!! WARNING: ARG 323 has a net charge of -0.9880 !!! WARNING: GLU 324 has a net charge of -1.2480 !!! WARNING: LYS 325 has a net charge of -0.1810 !!! WARNING: LYS 326 has a net charge of -0.1810 !!! WARNING: ALA 327 has a net charge of -0.2480 !!! WARNING: THR 328 has a net charge of -0.5580 !!! WARNING: GLN 329 has a net charge of -0.9360 !!! WARNING: MET 330 has a net charge of -0.2480 !!! WARNING: VAL 331 has a net charge of -0.2480 !!! WARNING: ALA 332 has a net charge of -0.2480 !!! WARNING: ILE 333 has a net charge of -0.2480 !!! WARNING: VAL 334 has a net charge of -0.2480 !!! WARNING: LEU 335 has a net charge of -0.2480 !!! WARNING: GLY 336 has a net charge of -0.2480 !!! WARNING: ALA 337 has a net charge of -0.2480 !!! WARNING: PHE 338 has a net charge of -0.2480 !!! WARNING: ILE 339 has a net charge of -0.2480 !!! WARNING: VAL 340 has a net charge of -0.2480 !!! WARNING: CYS 341 has a net charge of -0.3830 !!! WARNING: TRP 342 has a net charge of -0.5420 !!! WARNING: LEU 343 has a net charge of -0.2480 !!! WARNING: PHE 345 has a net charge of -0.2480 !!! WARNING: PHE 346 has a net charge of -0.2480 !!! WARNING: LEU 347 has a net charge of -0.2480 !!! WARNING: THR 348 has a net charge of -0.5580 !!! WARNING: HIE 349 has a net charge of -0.5680 !!! WARNING: VAL 350 has a net charge of -0.2480 !!! WARNING: LEU 351 has a net charge of -0.2480 !!! WARNING: ASN 352 has a net charge of -0.9360 !!! WARNING: THR 353 has a net charge of -0.5580 !!! WARNING: HIE 354 has a net charge of -0.5680 !!! WARNING: CYX 355 has a net charge of -0.2480 !!! WARNING: GLN 356 has a net charge of -0.9360 !!! WARNING: THR 357 has a net charge of -0.0150 !!! WARNING: CYX 358 has a net charge of -0.2480 !!! WARNING: HID 359 has a net charge of -0.5680 !!! WARNING: VAL 360 has a net charge of -0.2480 !!! WARNING: SER 361 has a net charge of -0.5580 !!! WARNING: GLU 363 has a net charge of -1.2480 !!! WARNING: LEU 364 has a net charge of -0.2480 !!! WARNING: TYR 365 has a net charge of -0.5870 !!! WARNING: SER 366 has a net charge of -0.5580 !!! WARNING: ALA 367 has a net charge of -0.2480 !!! WARNING: THR 368 has a net charge of -0.5580 !!! WARNING: THR 369 has a net charge of -0.5580 !!! WARNING: TRP 370 has a net charge of -0.5420 !!! WARNING: LEU 371 has a net charge of -0.2480 !!! WARNING: GLY 372 has a net charge of -0.2480 !!! WARNING: TYR 373 has a net charge of -0.5870 !!! WARNING: VAL 374 has a net charge of -0.2480 !!! WARNING: ASN 375 has a net charge of -0.9360 !!! WARNING: SER 376 has a net charge of -0.5580 !!! WARNING: ALA 377 has a net charge of -0.2480 !!! WARNING: LEU 378 has a net charge of -0.2480 !!! WARNING: ASN 379 has a net charge of -0.9360 !!! WARNING: VAL 381 has a net charge of -0.2480 !!! WARNING: ILE 382 has a net charge of -0.2480 !!! WARNING: TYR 383 has a net charge of -0.5870 !!! WARNING: THR 384 has a net charge of -0.5580 !!! WARNING: THR 385 has a net charge of -0.5580 !!! WARNING: PHE 386 has a net charge of -0.2480 !!! WARNING: ASN 387 has a net charge of -0.9360 !!! WARNING: ILE 388 has a net charge of -0.2480 !!! WARNING: GLU 389 has a net charge of -1.2480 !!! WARNING: PHE 390 has a net charge of -0.2480 !!! WARNING: ARG 391 has a net charge of -0.9880 !!! WARNING: LYS 392 has a net charge of -0.1810 !!! WARNING: ALA 393 has a net charge of -0.2480 !!! WARNING: PHE 394 has a net charge of -0.2480 !!! WARNING: LEU 395 has a net charge of -0.2480 !!! WARNING: LYS 396 has a net charge of -0.1810 !!! WARNING: ILE 397 has a net charge of -0.2480 !!! WARNING: LEU 398 has a net charge of -0.2480 !!! WARNING: SER 399 has a net charge of -0.5580 !!! WARNING: CYS 400 has a net charge of -0.3830 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: 1.669350 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -11.88000 52.09700 ymin,ymax (A): -14.78700 43.12200 zmin,zma (A): 4.503000 51.66100 x,y,z range (A): 63.97700 57.90900 47.15800 scale (grids/A): 1.669350 object centre (A): 20.10850 14.16750 28.08200 number of atom coordinates read : 2238 total number of charged atoms : 2107 net assigned charge : -113.9328 assigned positive charge : 259.5184 centred at (gu) : 91.11505 97.21318 91.25946 assigned negative charge : -373.4507 centred at (gu) : 90.97269 97.27537 91.19971 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25932 grid for indexing accessible points = 1.400000 m= 18676 mr = 37870 m= 2317 mr = 12276 m= 85 mr = 1184 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 29376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 16629 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) : 0.5564500 object centre at (A) : 20.10850 14.16750 28.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5978045E-02 -6.6097505E-02 midg,1,midg; midg,igrid,midg -5.0661787E-02 -0.1298234 1,midg,midg; igrid,midg,midg -0.1715306 -0.2111326 gauss-seidel spectral radius is 0.9982319 estimated iterations to convergence 189 setup time was (sec) 0.5700000 now iterating at: 14:29:59 rms-change max change #iterations 3.384937 143.6421 at 10iterations 1.406856 57.79072 at 20iterations 0.6154059 24.51758 at 30iterations 0.2784688 11.90201 at 40iterations 0.1363321 5.770111 at 50iterations 7.9183474E-02 3.636047 at 60iterations 5.1063512E-02 2.200500 at 70iterations 3.7292115E-02 1.572144 at 80iterations 2.8470073E-02 1.156006 at 90iterations 2.1425182E-02 0.8873291 at 100iterations 1.6274106E-02 0.6640015 at 110iterations 1.2467275E-02 0.5048523 at 120iterations finished qdiffx linear iterations at : 14:30:14 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 1.2467275E-02 0.5048523 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 14:30:15 8.328u 0.265s 0:16.46 52.1% 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 14:30:15 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2238 !!! WARNING: TYR 32 has a net charge of -0.5870 !!! WARNING: ALA 33 has a net charge of -0.2480 !!! WARNING: LEU 34 has a net charge of -0.2480 !!! WARNING: SER 35 has a net charge of -0.5580 !!! WARNING: TYR 36 has a net charge of -0.5870 !!! WARNING: CYS 37 has a net charge of -0.3830 !!! WARNING: ALA 38 has a net charge of -0.2480 !!! WARNING: LEU 39 has a net charge of -0.2480 !!! WARNING: ILE 40 has a net charge of -0.2480 !!! WARNING: LEU 41 has a net charge of -0.2480 !!! WARNING: ALA 42 has a net charge of -0.2480 !!! WARNING: ILE 43 has a net charge of -0.2480 !!! WARNING: VAL 44 has a net charge of -0.2480 !!! WARNING: PHE 45 has a net charge of -0.2480 !!! WARNING: GLY 46 has a net charge of -0.2480 !!! WARNING: ASN 47 has a net charge of -0.9360 !!! WARNING: GLY 48 has a net charge of -0.2480 !!! WARNING: LEU 49 has a net charge of -0.2480 !!! WARNING: VAL 50 has a net charge of -0.2480 !!! WARNING: CYS 51 has a net charge of -0.3830 !!! WARNING: MET 52 has a net charge of -0.2480 !!! WARNING: ALA 53 has a net charge of -0.2480 !!! WARNING: VAL 54 has a net charge of -0.2480 !!! WARNING: LEU 55 has a net charge of -0.2480 !!! WARNING: LYS 56 has a net charge of -0.1810 !!! WARNING: GLU 57 has a net charge of -1.2480 !!! WARNING: ARG 58 has a net charge of -0.9880 !!! WARNING: ALA 59 has a net charge of -0.2480 !!! WARNING: LEU 60 has a net charge of -0.2480 !!! WARNING: GLN 61 has a net charge of -0.9360 !!! WARNING: THR 62 has a net charge of -0.5580 !!! WARNING: THR 63 has a net charge of -0.5580 !!! WARNING: THR 64 has a net charge of -0.5580 !!! WARNING: ASN 65 has a net charge of -0.9360 !!! WARNING: TYR 66 has a net charge of -0.5870 !!! WARNING: LEU 67 has a net charge of -0.2480 !!! WARNING: VAL 68 has a net charge of -0.2480 !!! WARNING: VAL 69 has a net charge of -0.2480 !!! WARNING: SER 70 has a net charge of -0.5580 !!! WARNING: LEU 71 has a net charge of -0.2480 !!! WARNING: ALA 72 has a net charge of -0.2480 !!! WARNING: VAL 73 has a net charge of -0.2480 !!! WARNING: ALA 74 has a net charge of -0.2480 !!! WARNING: ASP 75 has a net charge of -1.2480 !!! WARNING: LEU 76 has a net charge of -0.2480 !!! WARNING: LEU 77 has a net charge of -0.2480 !!! WARNING: VAL 78 has a net charge of -0.2480 !!! WARNING: ALA 79 has a net charge of -0.2480 !!! WARNING: THR 80 has a net charge of -0.5580 !!! WARNING: LEU 81 has a net charge of -0.2480 !!! WARNING: VAL 82 has a net charge of -0.2480 !!! WARNING: MET 83 has a net charge of -0.2480 !!! WARNING: TRP 85 has a net charge of -0.5420 !!! WARNING: VAL 86 has a net charge of -0.2480 !!! WARNING: VAL 87 has a net charge of -0.2480 !!! WARNING: TYR 88 has a net charge of -0.5870 !!! WARNING: LEU 89 has a net charge of -0.2480 !!! WARNING: GLU 90 has a net charge of -1.2480 !!! WARNING: VAL 91 has a net charge of -0.2480 !!! WARNING: THR 92 has a net charge of -0.5580 !!! WARNING: GLY 93 has a net charge of -0.2480 !!! WARNING: GLY 94 has a net charge of -0.2480 !!! WARNING: VAL 95 has a net charge of -0.2480 !!! WARNING: TRP 96 has a net charge of -0.5420 !!! WARNING: ASN 97 has a net charge of -0.9360 !!! WARNING: PHE 98 has a net charge of -0.2480 !!! WARNING: SER 99 has a net charge of -0.5580 !!! WARNING: ARG 100 has a net charge of -0.9880 !!! WARNING: ILE 101 has a net charge of -0.2480 !!! WARNING: CYS 102 has a net charge of -0.3830 !!! WARNING: CYX 103 has a net charge of -0.2480 !!! WARNING: ASP 104 has a net charge of -1.2480 !!! WARNING: VAL 105 has a net charge of -0.2480 !!! WARNING: PHE 106 has a net charge of -0.2480 !!! WARNING: VAL 107 has a net charge of -0.2480 !!! WARNING: THR 108 has a net charge of -0.5580 !!! WARNING: LEU 109 has a net charge of -0.2480 !!! WARNING: ASP 110 has a net charge of -1.2480 !!! WARNING: VAL 111 has a net charge of -0.2480 !!! WARNING: MET 112 has a net charge of -0.2480 !!! WARNING: MET 113 has a net charge of -0.2480 !!! WARNING: CYS 114 has a net charge of -0.3830 !!! WARNING: THR 115 has a net charge of -0.5580 !!! WARNING: ALA 116 has a net charge of -0.2480 !!! WARNING: SER 117 has a net charge of -0.5580 !!! WARNING: ILE 118 has a net charge of -0.2480 !!! WARNING: TRP 119 has a net charge of -0.5420 !!! WARNING: ASN 120 has a net charge of -0.9360 !!! WARNING: LEU 121 has a net charge of -0.2480 !!! WARNING: CYS 122 has a net charge of -0.3830 !!! WARNING: ALA 123 has a net charge of -0.2480 !!! WARNING: ILE 124 has a net charge of -0.2480 !!! WARNING: SER 125 has a net charge of -0.5580 !!! WARNING: ILE 126 has a net charge of -0.2480 !!! WARNING: ASP 127 has a net charge of -1.2480 !!! WARNING: ARG 128 has a net charge of -0.9880 !!! WARNING: TYR 129 has a net charge of -0.5870 !!! WARNING: THR 130 has a net charge of -0.5580 !!! WARNING: ALA 131 has a net charge of -0.2480 !!! WARNING: VAL 132 has a net charge of -0.2480 !!! WARNING: VAL 133 has a net charge of -0.2480 !!! WARNING: MET 134 has a net charge of -0.2480 !!! WARNING: VAL 136 has a net charge of -0.2480 !!! WARNING: HID 137 has a net charge of -0.5680 !!! WARNING: TYR 138 has a net charge of -0.5870 !!! WARNING: GLN 139 has a net charge of -0.9360 !!! WARNING: HID 140 has a net charge of -0.5680 !!! WARNING: GLY 141 has a net charge of -0.2480 !!! WARNING: THR 142 has a net charge of -0.5580 !!! WARNING: GLY 143 has a net charge of -0.2480 !!! WARNING: GLN 144 has a net charge of -0.2310 !!! WARNING: SER 145 has a net charge of -0.0080 !!! WARNING: SER 146 has a net charge of -0.5580 !!! WARNING: CYS 147 has a net charge of -0.3830 !!! WARNING: ARG 148 has a net charge of -0.9880 !!! WARNING: ARG 149 has a net charge of -0.9880 !!! WARNING: VAL 150 has a net charge of -0.2480 !!! WARNING: ALA 151 has a net charge of -0.2480 !!! WARNING: LEU 152 has a net charge of -0.2480 !!! WARNING: MET 153 has a net charge of -0.2480 !!! WARNING: ILE 154 has a net charge of -0.2480 !!! WARNING: THR 155 has a net charge of -0.5580 !!! WARNING: ALA 156 has a net charge of -0.2480 !!! WARNING: VAL 157 has a net charge of -0.2480 !!! WARNING: TRP 158 has a net charge of -0.5420 !!! WARNING: VAL 159 has a net charge of -0.2480 !!! WARNING: LEU 160 has a net charge of -0.2480 !!! WARNING: ALA 161 has a net charge of -0.2480 !!! WARNING: PHE 162 has a net charge of -0.2480 !!! WARNING: ALA 163 has a net charge of -0.2480 !!! WARNING: VAL 164 has a net charge of -0.2480 !!! WARNING: SER 165 has a net charge of -0.5580 !!! WARNING: CYS 166 has a net charge of -0.3830 !!! WARNING: LEU 168 has a net charge of -0.2480 !!! WARNING: LEU 169 has a net charge of -0.2480 !!! WARNING: PHE 170 has a net charge of -0.2480 !!! WARNING: GLY 171 has a net charge of -0.2480 !!! WARNING: PHE 172 has a net charge of -0.2480 !!! WARNING: ASN 173 has a net charge of -0.9360 !!! WARNING: THR 174 has a net charge of -0.5580 !!! WARNING: THR 175 has a net charge of -0.5580 !!! WARNING: GLY 176 has a net charge of -0.2480 !!! WARNING: ASP 177 has a net charge of -1.2480 !!! WARNING: THR 179 has a net charge of -0.5580 !!! WARNING: VAL 180 has a net charge of -0.2480 !!! WARNING: CYX 181 has a net charge of -0.2480 !!! WARNING: SER 182 has a net charge of -0.5580 !!! WARNING: ILE 183 has a net charge of -0.2480 !!! WARNING: SER 184 has a net charge of -0.5580 !!! WARNING: ASN 185 has a net charge of -0.9360 !!! WARNING: ASP 187 has a net charge of -1.2480 !!! WARNING: PHE 188 has a net charge of -0.2480 !!! WARNING: VAL 189 has a net charge of -0.2480 !!! WARNING: ILE 190 has a net charge of -0.2480 !!! WARNING: TYR 191 has a net charge of -0.5870 !!! WARNING: SER 192 has a net charge of -0.5580 !!! WARNING: SER 193 has a net charge of -0.5580 !!! WARNING: VAL 194 has a net charge of -0.2480 !!! WARNING: VAL 195 has a net charge of -0.2480 !!! WARNING: SER 196 has a net charge of -0.5580 !!! WARNING: PHE 197 has a net charge of -0.2480 !!! WARNING: TYR 198 has a net charge of -0.5870 !!! WARNING: LEU 199 has a net charge of -0.2480 !!! WARNING: PHE 201 has a net charge of -0.2480 !!! WARNING: GLY 202 has a net charge of -0.2480 !!! WARNING: VAL 203 has a net charge of -0.2480 !!! WARNING: THR 204 has a net charge of -0.5580 !!! WARNING: VAL 205 has a net charge of -0.2480 !!! WARNING: LEU 206 has a net charge of -0.2480 !!! WARNING: VAL 207 has a net charge of -0.2480 !!! WARNING: TYR 208 has a net charge of -0.5870 !!! WARNING: ALA 209 has a net charge of -0.2480 !!! WARNING: ARG 210 has a net charge of -0.9880 !!! WARNING: ILE 211 has a net charge of -0.2480 !!! WARNING: TYR 212 has a net charge of -0.5870 !!! WARNING: VAL 213 has a net charge of -0.2480 !!! WARNING: VAL 214 has a net charge of -0.2480 !!! WARNING: LEU 215 has a net charge of -0.2480 !!! WARNING: LYS 216 has a net charge of -0.1810 !!! WARNING: GLN 217 has a net charge of -0.9360 !!! WARNING: ARG 218 has a net charge of -0.9880 !!! WARNING: ARG 219 has a net charge of -0.9880 !!! WARNING: ARG 220 has a net charge of -0.9880 !!! WARNING: LYS 221 has a net charge of -0.1810 !!! WARNING: GLY 319 has a net charge of -0.2480 !!! WARNING: VAL 320 has a net charge of -0.2480 !!! WARNING: LEU 322 has a net charge of -0.2480 !!! WARNING: ARG 323 has a net charge of -0.9880 !!! WARNING: GLU 324 has a net charge of -1.2480 !!! WARNING: LYS 325 has a net charge of -0.1810 !!! WARNING: LYS 326 has a net charge of -0.1810 !!! WARNING: ALA 327 has a net charge of -0.2480 !!! WARNING: THR 328 has a net charge of -0.5580 !!! WARNING: GLN 329 has a net charge of -0.9360 !!! WARNING: MET 330 has a net charge of -0.2480 !!! WARNING: VAL 331 has a net charge of -0.2480 !!! WARNING: ALA 332 has a net charge of -0.2480 !!! WARNING: ILE 333 has a net charge of -0.2480 !!! WARNING: VAL 334 has a net charge of -0.2480 !!! WARNING: LEU 335 has a net charge of -0.2480 !!! WARNING: GLY 336 has a net charge of -0.2480 !!! WARNING: ALA 337 has a net charge of -0.2480 !!! WARNING: PHE 338 has a net charge of -0.2480 !!! WARNING: ILE 339 has a net charge of -0.2480 !!! WARNING: VAL 340 has a net charge of -0.2480 !!! WARNING: CYS 341 has a net charge of -0.3830 !!! WARNING: TRP 342 has a net charge of -0.5420 !!! WARNING: LEU 343 has a net charge of -0.2480 !!! WARNING: PHE 345 has a net charge of -0.2480 !!! WARNING: PHE 346 has a net charge of -0.2480 !!! WARNING: LEU 347 has a net charge of -0.2480 !!! WARNING: THR 348 has a net charge of -0.5580 !!! WARNING: HIE 349 has a net charge of -0.5680 !!! WARNING: VAL 350 has a net charge of -0.2480 !!! WARNING: LEU 351 has a net charge of -0.2480 !!! WARNING: ASN 352 has a net charge of -0.9360 !!! WARNING: THR 353 has a net charge of -0.5580 !!! WARNING: HIE 354 has a net charge of -0.5680 !!! WARNING: CYX 355 has a net charge of -0.2480 !!! WARNING: GLN 356 has a net charge of -0.9360 !!! WARNING: THR 357 has a net charge of -0.0150 !!! WARNING: CYX 358 has a net charge of -0.2480 !!! WARNING: HID 359 has a net charge of -0.5680 !!! WARNING: VAL 360 has a net charge of -0.2480 !!! WARNING: SER 361 has a net charge of -0.5580 !!! WARNING: GLU 363 has a net charge of -1.2480 !!! WARNING: LEU 364 has a net charge of -0.2480 !!! WARNING: TYR 365 has a net charge of -0.5870 !!! WARNING: SER 366 has a net charge of -0.5580 !!! WARNING: ALA 367 has a net charge of -0.2480 !!! WARNING: THR 368 has a net charge of -0.5580 !!! WARNING: THR 369 has a net charge of -0.5580 !!! WARNING: TRP 370 has a net charge of -0.5420 !!! WARNING: LEU 371 has a net charge of -0.2480 !!! WARNING: GLY 372 has a net charge of -0.2480 !!! WARNING: TYR 373 has a net charge of -0.5870 !!! WARNING: VAL 374 has a net charge of -0.2480 !!! WARNING: ASN 375 has a net charge of -0.9360 !!! WARNING: SER 376 has a net charge of -0.5580 !!! WARNING: ALA 377 has a net charge of -0.2480 !!! WARNING: LEU 378 has a net charge of -0.2480 !!! WARNING: ASN 379 has a net charge of -0.9360 !!! WARNING: VAL 381 has a net charge of -0.2480 !!! WARNING: ILE 382 has a net charge of -0.2480 !!! WARNING: TYR 383 has a net charge of -0.5870 !!! WARNING: THR 384 has a net charge of -0.5580 !!! WARNING: THR 385 has a net charge of -0.5580 !!! WARNING: PHE 386 has a net charge of -0.2480 !!! WARNING: ASN 387 has a net charge of -0.9360 !!! WARNING: ILE 388 has a net charge of -0.2480 !!! WARNING: GLU 389 has a net charge of -1.2480 !!! WARNING: PHE 390 has a net charge of -0.2480 !!! WARNING: ARG 391 has a net charge of -0.9880 !!! WARNING: LYS 392 has a net charge of -0.1810 !!! WARNING: ALA 393 has a net charge of -0.2480 !!! WARNING: PHE 394 has a net charge of -0.2480 !!! WARNING: LEU 395 has a net charge of -0.2480 !!! WARNING: LYS 396 has a net charge of -0.1810 !!! WARNING: ILE 397 has a net charge of -0.2480 !!! WARNING: LEU 398 has a net charge of -0.2480 !!! WARNING: SER 399 has a net charge of -0.5580 !!! WARNING: CYS 400 has a net charge of -0.3830 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: 2.504025 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -11.88000 52.09700 ymin,ymax (A): -14.78700 43.12200 zmin,zma (A): 4.503000 51.66100 x,y,z range (A): 63.97700 57.90900 47.15800 scale (grids/A): 2.504025 object centre (A): 20.10850 14.16750 28.08200 number of atom coordinates read : 2238 total number of charged atoms : 2107 net assigned charge : -113.9328 assigned positive charge : 259.5184 centred at (gu) : 91.67259 100.8200 91.88925 assigned negative charge : -373.4507 centred at (gu) : 91.45898 100.9131 91.79961 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 138127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25932 grid for indexing accessible points = 1.400000 m= 61720 mr = 93227 m= 19953 mr = 47101 m= 3676 mr = 14676 m= 308 mr = 2463 m= 14 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 66193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 16856 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) : 1.669350 object centre at (A) : 20.10850 14.16750 28.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6490985 -0.7668775 midg,1,midg; midg,igrid,midg -0.5936226 -1.533845 1,midg,midg; igrid,midg,midg -2.375768 -3.143571 gauss-seidel spectral radius is 0.9991404 estimated iterations to convergence 269 setup time was (sec) 1.000000 now iterating at: 14:30:16 rms-change max change #iterations 7.978361 319.2253 at 10iterations 4.430209 120.1972 at 20iterations 2.445489 55.33762 at 30iterations 1.354751 29.18340 at 40iterations 0.7505199 16.55554 at 50iterations 0.4133591 10.38098 at 60iterations 0.2291380 4.868782 at 70iterations 0.1288420 3.154419 at 80iterations 7.3455259E-02 2.000061 at 90iterations 4.2915612E-02 0.9572144 at 100iterations 2.6356487E-02 0.6522522 at 110iterations 1.8047655E-02 0.4573364 at 120iterations 1.3641554E-02 0.3322754 at 130iterations 1.0860705E-02 0.2569580 at 140iterations 8.8074701E-03 0.1981201 at 150iterations 7.2993515E-03 0.1671753 at 160iterations 6.1452189E-03 0.1378479 at 170iterations 5.2042287E-03 0.1155396 at 180iterations finished qdiffx linear iterations at : 14:30:40 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 5.2042287E-03 0.1155396 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 14:30:40 13.150u 0.244s 0:25.46 52.5% 0+0k 0+0io 0pf+0w