Sat Oct 8 13:39:26 PDT 2011 #!/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+sph2.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 = amb2.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 Sat Oct 8 2011 at 13:39:26 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 446 !!! WARNING: SER 2 has a net charge of 0.2920 !!! WARNING: ARG 3 has a net charge of 0.2370 !!! WARNING: LEU 4 has a net charge of 0.2040 !!! WARNING: LEU 5 has a net charge of 0.2040 !!! WARNING: LEU 6 has a net charge of 0.2040 !!! WARNING: ASN 7 has a net charge of 0.2170 !!! WARNING: ASN 8 has a net charge of 0.2170 !!! WARNING: ALA 10 has a net charge of 0.2150 !!! WARNING: LYS 11 has a net charge of 0.2270 !!! WARNING: MET 12 has a net charge of 0.1370 !!! WARNING: PRO 13 has a net charge of 0.1120 !!! WARNING: ILE 14 has a net charge of 0.1990 !!! WARNING: LEU 15 has a net charge of 0.2040 !!! WARNING: GLY 16 has a net charge of 0.2460 !!! WARNING: LEU 17 has a net charge of 0.2040 !!! WARNING: GLY 18 has a net charge of 0.2460 !!! WARNING: THR 19 has a net charge of 0.2680 !!! WARNING: TRP 20 has a net charge of 0.2480 !!! WARNING: LYS 21 has a net charge of 0.2270 !!! WARNING: SER 22 has a net charge of 0.2920 !!! WARNING: PRO 23 has a net charge of 0.1120 !!! WARNING: PRO 24 has a net charge of 0.1120 !!! WARNING: GLY 25 has a net charge of 0.2460 !!! WARNING: GLN 26 has a net charge of 0.2100 !!! WARNING: VAL 27 has a net charge of 0.2010 !!! WARNING: THR 28 has a net charge of 0.2680 !!! WARNING: GLU 29 has a net charge of 0.2460 !!! WARNING: ALA 30 has a net charge of 0.2150 !!! WARNING: VAL 31 has a net charge of 0.2010 !!! WARNING: LYS 32 has a net charge of 0.2270 !!! WARNING: VAL 33 has a net charge of 0.2010 !!! WARNING: ALA 34 has a net charge of 0.2150 !!! WARNING: ILE 35 has a net charge of 0.1990 !!! WARNING: VAL 37 has a net charge of 0.2010 !!! WARNING: GLY 38 has a net charge of 0.2460 !!! WARNING: TYR 39 has a net charge of 0.2450 !!! WARNING: ARG 40 has a net charge of 0.2370 !!! WARNING: ILE 42 has a net charge of 0.1990 !!! WARNING: ASP 43 has a net charge of 0.2460 !!! WARNING: CYS 44 has a net charge of 0.1460 !!! WARNING: ALA 45 has a net charge of 0.2150 !!! WARNING: VAL 47 has a net charge of 0.2010 !!! WARNING: TYR 48 has a net charge of 0.2450 !!! WARNING: GLN 49 has a net charge of 0.2100 !!! WARNING: ASN 50 has a net charge of 0.2170 !!! WARNING: GLU 51 has a net charge of 0.2460 !!! WARNING: ASN 52 has a net charge of 0.2170 !!! WARNING: GLU 53 has a net charge of 0.2460 !!! WARNING: VAL 54 has a net charge of 0.2010 !!! WARNING: GLY 55 has a net charge of 0.2460 !!! WARNING: VAL 56 has a net charge of 0.2010 !!! WARNING: ALA 57 has a net charge of 0.2150 !!! WARNING: ILE 58 has a net charge of 0.1990 !!! WARNING: GLN 59 has a net charge of 0.2100 !!! WARNING: GLU 60 has a net charge of 0.2460 !!! WARNING: ARG 69 has a net charge of 0.2370 !!! WARNING: GLU 70 has a net charge of 0.2460 !!! WARNING: GLU 71 has a net charge of 0.2460 !!! WARNING: LEU 72 has a net charge of 0.2040 !!! WARNING: PHE 73 has a net charge of 0.2140 !!! WARNING: ILE 74 has a net charge of 0.1990 !!! WARNING: VAL 75 has a net charge of 0.2010 !!! WARNING: SER 76 has a net charge of 0.2920 !!! WARNING: LYS 77 has a net charge of 0.2270 !!! WARNING: LEU 78 has a net charge of 0.2040 !!! WARNING: TRP 79 has a net charge of 0.2480 !!! WARNING: CYS 80 has a net charge of 0.1460 !!! WARNING: THR 81 has a net charge of 0.2680 !!! WARNING: TYR 82 has a net charge of 0.2450 !!! WARNING: GLU 84 has a net charge of 0.2460 !!! WARNING: LYS 85 has a net charge of 0.2270 !!! WARNING: GLY 86 has a net charge of 0.2460 !!! WARNING: LEU 87 has a net charge of 0.2040 !!! WARNING: VAL 88 has a net charge of 0.2010 !!! WARNING: LYS 89 has a net charge of 0.2270 !!! WARNING: GLY 90 has a net charge of 0.2460 !!! WARNING: ALA 91 has a net charge of 0.2150 !!! WARNING: CYS 92 has a net charge of 0.1460 !!! WARNING: GLN 93 has a net charge of 0.2100 !!! WARNING: LYS 94 has a net charge of 0.2270 !!! WARNING: THR 95 has a net charge of 0.2680 !!! WARNING: LEU 96 has a net charge of 0.2040 !!! WARNING: SER 97 has a net charge of 0.2920 !!! WARNING: ASP 98 has a net charge of 0.2460 !!! WARNING: LEU 99 has a net charge of 0.2040 !!! WARNING: LYS 100 has a net charge of 0.2270 !!! WARNING: LEU 101 has a net charge of 0.2040 !!! WARNING: ASP 102 has a net charge of 0.2460 !!! WARNING: TYR 103 has a net charge of 0.2450 !!! WARNING: LEU 104 has a net charge of 0.2040 !!! WARNING: ASP 105 has a net charge of 0.2460 !!! WARNING: LEU 106 has a net charge of 0.2040 !!! WARNING: TYR 107 has a net charge of 0.2450 !!! WARNING: LEU 108 has a net charge of 0.2040 !!! WARNING: ILE 109 has a net charge of 0.1990 !!! WARNING: TRP 111 has a net charge of 0.2480 !!! WARNING: PRO 112 has a net charge of 0.1120 !!! WARNING: THR 113 has a net charge of 0.2680 !!! WARNING: GLY 114 has a net charge of 0.2460 !!! WARNING: PHE 115 has a net charge of 0.2140 !!! WARNING: LYS 116 has a net charge of 0.2270 !!! WARNING: PRO 117 has a net charge of 0.1120 !!! WARNING: GLY 118 has a net charge of 0.2460 !!! WARNING: LYS 119 has a net charge of 0.2270 !!! WARNING: GLU 120 has a net charge of 0.2460 !!! WARNING: PHE 121 has a net charge of 0.2140 !!! WARNING: PHE 122 has a net charge of 0.2140 !!! WARNING: PRO 123 has a net charge of 0.1120 !!! WARNING: LEU 124 has a net charge of 0.2040 !!! WARNING: ASP 125 has a net charge of 0.2460 !!! WARNING: GLU 126 has a net charge of 0.2460 !!! WARNING: SER 127 has a net charge of 0.2920 !!! WARNING: GLY 128 has a net charge of 0.2460 !!! WARNING: ASN 129 has a net charge of 0.2170 !!! WARNING: VAL 130 has a net charge of 0.2010 !!! WARNING: VAL 131 has a net charge of 0.2010 !!! WARNING: PRO 132 has a net charge of 0.1120 !!! WARNING: SER 133 has a net charge of 0.2920 !!! WARNING: ASP 134 has a net charge of 0.2460 !!! WARNING: THR 135 has a net charge of 0.2680 !!! WARNING: ASN 136 has a net charge of 0.2170 !!! WARNING: ILE 137 has a net charge of 0.1990 !!! WARNING: LEU 138 has a net charge of 0.2040 !!! WARNING: ASP 139 has a net charge of 0.2460 !!! WARNING: THR 140 has a net charge of 0.2680 !!! WARNING: TRP 141 has a net charge of 0.2480 !!! WARNING: ALA 142 has a net charge of 0.2150 !!! WARNING: ALA 143 has a net charge of 0.2150 !!! WARNING: MET 144 has a net charge of 0.1370 !!! WARNING: GLU 145 has a net charge of 0.2460 !!! WARNING: GLU 146 has a net charge of 0.2460 !!! WARNING: LEU 147 has a net charge of 0.2040 !!! WARNING: VAL 148 has a net charge of 0.2010 !!! WARNING: GLY 151 has a net charge of 0.2460 !!! WARNING: LEU 152 has a net charge of 0.2040 !!! WARNING: VAL 153 has a net charge of 0.2010 !!! WARNING: LYS 154 has a net charge of 0.2270 !!! WARNING: ALA 155 has a net charge of 0.2150 !!! WARNING: ILE 156 has a net charge of 0.1990 !!! WARNING: GLY 157 has a net charge of 0.2460 !!! WARNING: ILE 158 has a net charge of 0.1990 !!! WARNING: SER 159 has a net charge of 0.2920 !!! WARNING: ASN 160 has a net charge of 0.2170 !!! WARNING: PHE 161 has a net charge of 0.2140 !!! WARNING: ASN 162 has a net charge of 0.2170 !!! WARNING: LEU 164 has a net charge of 0.2040 !!! WARNING: GLN 165 has a net charge of 0.2100 !!! WARNING: VAL 166 has a net charge of 0.2010 !!! WARNING: GLU 167 has a net charge of 0.2460 !!! WARNING: MET 168 has a net charge of 0.1370 !!! WARNING: ILE 169 has a net charge of 0.1990 !!! WARNING: LEU 170 has a net charge of 0.2040 !!! WARNING: ASN 171 has a net charge of 0.2170 !!! WARNING: LYS 172 has a net charge of 0.2270 !!! WARNING: PRO 173 has a net charge of 0.1120 !!! WARNING: LEU 175 has a net charge of 0.2040 !!! WARNING: LYS 176 has a net charge of 0.2270 !!! WARNING: TYR 177 has a net charge of 0.2450 !!! WARNING: LYS 178 has a net charge of 0.2270 !!! WARNING: PRO 179 has a net charge of 0.1120 !!! WARNING: ALA 180 has a net charge of 0.2150 !!! WARNING: VAL 181 has a net charge of 0.2010 !!! WARNING: ASN 182 has a net charge of 0.2170 !!! WARNING: GLN 183 has a net charge of 0.2100 !!! WARNING: ILE 184 has a net charge of 0.1990 !!! WARNING: GLU 185 has a net charge of 0.2460 !!! WARNING: CYS 186 has a net charge of 0.1460 !!! WARNING: PRO 188 has a net charge of 0.1120 !!! WARNING: TYR 189 has a net charge of 0.2450 !!! WARNING: LEU 190 has a net charge of 0.2040 !!! WARNING: THR 191 has a net charge of 0.2680 !!! WARNING: GLN 192 has a net charge of 0.2100 !!! WARNING: GLU 193 has a net charge of 0.2460 !!! WARNING: LYS 194 has a net charge of 0.2270 !!! WARNING: LEU 195 has a net charge of 0.2040 !!! WARNING: ILE 196 has a net charge of 0.1990 !!! WARNING: GLN 197 has a net charge of 0.2100 !!! WARNING: TYR 198 has a net charge of 0.2450 !!! WARNING: CYS 199 has a net charge of 0.1460 !!! WARNING: GLN 200 has a net charge of 0.2100 !!! WARNING: SER 201 has a net charge of 0.2920 !!! WARNING: LYS 202 has a net charge of 0.2270 !!! WARNING: GLY 203 has a net charge of 0.2460 !!! WARNING: ILE 204 has a net charge of 0.1990 !!! WARNING: VAL 205 has a net charge of 0.2010 !!! WARNING: VAL 206 has a net charge of 0.2010 !!! WARNING: THR 207 has a net charge of 0.2680 !!! WARNING: ALA 208 has a net charge of 0.2150 !!! WARNING: TYR 209 has a net charge of 0.2450 !!! WARNING: SER 210 has a net charge of 0.2920 !!! WARNING: PRO 211 has a net charge of 0.1120 !!! WARNING: LEU 212 has a net charge of 0.2040 !!! WARNING: GLY 213 has a net charge of 0.2460 !!! WARNING: SER 214 has a net charge of 0.2920 !!! WARNING: PRO 215 has a net charge of 0.1120 !!! WARNING: ASP 216 has a net charge of 0.2460 !!! WARNING: ARG 217 has a net charge of 0.2370 !!! WARNING: PRO 218 has a net charge of 0.1120 !!! WARNING: TRP 219 has a net charge of 0.2480 !!! WARNING: ALA 220 has a net charge of 0.2150 !!! WARNING: LYS 221 has a net charge of 0.2270 !!! WARNING: PRO 222 has a net charge of 0.1120 !!! WARNING: GLU 223 has a net charge of 0.2460 !!! WARNING: ASP 224 has a net charge of 0.2460 !!! WARNING: PRO 225 has a net charge of 0.1120 !!! WARNING: SER 226 has a net charge of 0.2920 !!! WARNING: LEU 227 has a net charge of 0.2040 !!! WARNING: LEU 228 has a net charge of 0.2040 !!! WARNING: GLU 229 has a net charge of 0.2460 !!! WARNING: ASP 230 has a net charge of 0.2460 !!! WARNING: ILE 233 has a net charge of 0.1990 !!! WARNING: THR 243 has a net charge of 0.2680 !!! WARNING: THR 244 has a net charge of 0.2680 !!! WARNING: ALA 245 has a net charge of 0.2150 !!! WARNING: GLN 246 has a net charge of 0.2100 !!! WARNING: VAL 247 has a net charge of 0.2010 !!! WARNING: LEU 248 has a net charge of 0.2040 !!! WARNING: ILE 249 has a net charge of 0.1990 !!! WARNING: ARG 250 has a net charge of 0.2370 !!! WARNING: PHE 251 has a net charge of 0.2140 !!! WARNING: PRO 252 has a net charge of 0.1120 !!! WARNING: MET 253 has a net charge of 0.1370 !!! WARNING: GLN 254 has a net charge of 0.2100 !!! WARNING: ARG 255 has a net charge of 0.2370 !!! WARNING: ASN 256 has a net charge of 0.2170 !!! WARNING: LEU 257 has a net charge of 0.2040 !!! WARNING: VAL 258 has a net charge of 0.2010 !!! WARNING: VAL 259 has a net charge of 0.2010 !!! WARNING: ILE 260 has a net charge of 0.1990 !!! WARNING: PRO 261 has a net charge of 0.1120 !!! WARNING: LYS 262 has a net charge of 0.2270 !!! WARNING: SER 263 has a net charge of 0.2920 !!! WARNING: VAL 264 has a net charge of 0.2010 !!! WARNING: THR 265 has a net charge of 0.2680 !!! WARNING: PRO 266 has a net charge of 0.1120 !!! WARNING: GLU 267 has a net charge of 0.2460 !!! WARNING: ARG 268 has a net charge of 0.2370 !!! WARNING: ILE 269 has a net charge of 0.1990 !!! WARNING: ALA 270 has a net charge of 0.2150 !!! WARNING: GLU 271 has a net charge of 0.2460 !!! WARNING: ASN 272 has a net charge of 0.2170 !!! WARNING: PHE 273 has a net charge of 0.2140 !!! WARNING: LYS 274 has a net charge of 0.2270 !!! WARNING: VAL 275 has a net charge of 0.2010 !!! WARNING: LEU 288 has a net charge of 0.2040 !!! WARNING: LEU 289 has a net charge of 0.2040 !!! WARNING: SER 290 has a net charge of 0.2920 !!! WARNING: TYR 291 has a net charge of 0.2450 !!! WARNING: ASN 292 has a net charge of 0.2170 !!! WARNING: ARG 293 has a net charge of 0.2370 !!! WARNING: ASN 294 has a net charge of 0.2170 !!! WARNING: TRP 295 has a net charge of 0.2480 !!! WARNING: ARG 296 has a net charge of 0.2370 !!! WARNING: VAL 297 has a net charge of 0.2010 !!! WARNING: CYS 298 has a net charge of 0.1460 !!! WARNING: ALA 299 has a net charge of 0.2150 !!! WARNING: LEU 300 has a net charge of 0.2040 !!! WARNING: LEU 301 has a net charge of 0.2040 !!! WARNING: SER 302 has a net charge of 0.2920 !!! WARNING: CYS 303 has a net charge of 0.1460 !!! WARNING: THR 304 has a net charge of 0.2680 !!! WARNING: SER 305 has a net charge of 0.2920 !!! WARNING: LYS 307 has a net charge of 0.2270 !!! WARNING: ASP 308 has a net charge of 0.2460 !!! WARNING: TYR 309 has a net charge of 0.2450 !!! WARNING: PRO 310 has a net charge of 0.1120 !!! WARNING: PHE 311 has a net charge of 0.2140 !!! WARNING: GLU 313 has a net charge of 0.2460 !!! WARNING: GLU 314 has a net charge of 0.2460 !!! WARNING: PHE 315 has a net charge of 0.2140 !!! WARNING: NAP 350 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 0.7023774 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): 41.94700 91.94300 ymin,ymax (A): -58.12200 -12.22000 zmin,zma (A): -29.04600 21.63900 x,y,z range (A): 49.99600 45.90200 50.68500 scale (grids/A): 0.7023774 object centre (A): 66.94500 -35.17100 -3.703501 number of atom coordinates read : 446 total number of charged atoms : 326 net assigned charge : 58.27298 assigned positive charge : 71.27699 centred at (gu) : 91.51471 91.54794 90.46281 assigned negative charge : -13.00400 centred at (gu) : 95.25084 90.38099 97.25111 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5074 nv = 96 ne = 84 npr = 5347 no. pairs analyzed = 5347 no. exposed pairs = 1167 no. arc points = 20949 no. surface atoms = 375 nbur = 71 mkacc time = 2.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 560 mr = 911 m= 18 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1300000 number of dielectric boundary points 4688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1139 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 2416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6208172E-07 2.0650873E-07 midg,1,midg; midg,igrid,midg 3.1375194E-07 6.1686904E-07 1,midg,midg; igrid,midg,midg 3.6515485E-07 4.6039651E-07 gauss-seidel spectral radius is 0.9894212 estimated iterations to convergence 79 setup time was (sec) 0.4500000 now iterating at: 13:39:26 rms-change max change #iterations 7.4704982E-02 29.69549 at 10iterations 1.0187755E-02 2.953011 at 20iterations 2.0176873E-03 0.3392601 at 30iterations 5.4403424E-04 5.1643372E-02 at 40iterations 1.5712605E-04 8.8367462E-03 at 50iterations finished qdiffx linear iterations at : 13:39:31 total time elapsed so far: 4.840000 # loops : 50 mean,max change (kT/e) : 1.5712605E-04 8.8367462E-03 energy calculations done at 4.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 13:39:31 5.011u 0.468s 0:05.74 95.2% 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 Sat Oct 8 2011 at 13:39:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 446 !!! WARNING: SER 2 has a net charge of 0.2920 !!! WARNING: ARG 3 has a net charge of 0.2370 !!! WARNING: LEU 4 has a net charge of 0.2040 !!! WARNING: LEU 5 has a net charge of 0.2040 !!! WARNING: LEU 6 has a net charge of 0.2040 !!! WARNING: ASN 7 has a net charge of 0.2170 !!! WARNING: ASN 8 has a net charge of 0.2170 !!! WARNING: ALA 10 has a net charge of 0.2150 !!! WARNING: LYS 11 has a net charge of 0.2270 !!! WARNING: MET 12 has a net charge of 0.1370 !!! WARNING: PRO 13 has a net charge of 0.1120 !!! WARNING: ILE 14 has a net charge of 0.1990 !!! WARNING: LEU 15 has a net charge of 0.2040 !!! WARNING: GLY 16 has a net charge of 0.2460 !!! WARNING: LEU 17 has a net charge of 0.2040 !!! WARNING: GLY 18 has a net charge of 0.2460 !!! WARNING: THR 19 has a net charge of 0.2680 !!! WARNING: TRP 20 has a net charge of 0.2480 !!! WARNING: LYS 21 has a net charge of 0.2270 !!! WARNING: SER 22 has a net charge of 0.2920 !!! WARNING: PRO 23 has a net charge of 0.1120 !!! WARNING: PRO 24 has a net charge of 0.1120 !!! WARNING: GLY 25 has a net charge of 0.2460 !!! WARNING: GLN 26 has a net charge of 0.2100 !!! WARNING: VAL 27 has a net charge of 0.2010 !!! WARNING: THR 28 has a net charge of 0.2680 !!! WARNING: GLU 29 has a net charge of 0.2460 !!! WARNING: ALA 30 has a net charge of 0.2150 !!! WARNING: VAL 31 has a net charge of 0.2010 !!! WARNING: LYS 32 has a net charge of 0.2270 !!! WARNING: VAL 33 has a net charge of 0.2010 !!! WARNING: ALA 34 has a net charge of 0.2150 !!! WARNING: ILE 35 has a net charge of 0.1990 !!! WARNING: VAL 37 has a net charge of 0.2010 !!! WARNING: GLY 38 has a net charge of 0.2460 !!! WARNING: TYR 39 has a net charge of 0.2450 !!! WARNING: ARG 40 has a net charge of 0.2370 !!! WARNING: ILE 42 has a net charge of 0.1990 !!! WARNING: ASP 43 has a net charge of 0.2460 !!! WARNING: CYS 44 has a net charge of 0.1460 !!! WARNING: ALA 45 has a net charge of 0.2150 !!! WARNING: VAL 47 has a net charge of 0.2010 !!! WARNING: TYR 48 has a net charge of 0.2450 !!! WARNING: GLN 49 has a net charge of 0.2100 !!! WARNING: ASN 50 has a net charge of 0.2170 !!! WARNING: GLU 51 has a net charge of 0.2460 !!! WARNING: ASN 52 has a net charge of 0.2170 !!! WARNING: GLU 53 has a net charge of 0.2460 !!! WARNING: VAL 54 has a net charge of 0.2010 !!! WARNING: GLY 55 has a net charge of 0.2460 !!! WARNING: VAL 56 has a net charge of 0.2010 !!! WARNING: ALA 57 has a net charge of 0.2150 !!! WARNING: ILE 58 has a net charge of 0.1990 !!! WARNING: GLN 59 has a net charge of 0.2100 !!! WARNING: GLU 60 has a net charge of 0.2460 !!! WARNING: ARG 69 has a net charge of 0.2370 !!! WARNING: GLU 70 has a net charge of 0.2460 !!! WARNING: GLU 71 has a net charge of 0.2460 !!! WARNING: LEU 72 has a net charge of 0.2040 !!! WARNING: PHE 73 has a net charge of 0.2140 !!! WARNING: ILE 74 has a net charge of 0.1990 !!! WARNING: VAL 75 has a net charge of 0.2010 !!! WARNING: SER 76 has a net charge of 0.2920 !!! WARNING: LYS 77 has a net charge of 0.2270 !!! WARNING: LEU 78 has a net charge of 0.2040 !!! WARNING: TRP 79 has a net charge of 0.2480 !!! WARNING: CYS 80 has a net charge of 0.1460 !!! WARNING: THR 81 has a net charge of 0.2680 !!! WARNING: TYR 82 has a net charge of 0.2450 !!! WARNING: GLU 84 has a net charge of 0.2460 !!! WARNING: LYS 85 has a net charge of 0.2270 !!! WARNING: GLY 86 has a net charge of 0.2460 !!! WARNING: LEU 87 has a net charge of 0.2040 !!! WARNING: VAL 88 has a net charge of 0.2010 !!! WARNING: LYS 89 has a net charge of 0.2270 !!! WARNING: GLY 90 has a net charge of 0.2460 !!! WARNING: ALA 91 has a net charge of 0.2150 !!! WARNING: CYS 92 has a net charge of 0.1460 !!! WARNING: GLN 93 has a net charge of 0.2100 !!! WARNING: LYS 94 has a net charge of 0.2270 !!! WARNING: THR 95 has a net charge of 0.2680 !!! WARNING: LEU 96 has a net charge of 0.2040 !!! WARNING: SER 97 has a net charge of 0.2920 !!! WARNING: ASP 98 has a net charge of 0.2460 !!! WARNING: LEU 99 has a net charge of 0.2040 !!! WARNING: LYS 100 has a net charge of 0.2270 !!! WARNING: LEU 101 has a net charge of 0.2040 !!! WARNING: ASP 102 has a net charge of 0.2460 !!! WARNING: TYR 103 has a net charge of 0.2450 !!! WARNING: LEU 104 has a net charge of 0.2040 !!! WARNING: ASP 105 has a net charge of 0.2460 !!! WARNING: LEU 106 has a net charge of 0.2040 !!! WARNING: TYR 107 has a net charge of 0.2450 !!! WARNING: LEU 108 has a net charge of 0.2040 !!! WARNING: ILE 109 has a net charge of 0.1990 !!! WARNING: TRP 111 has a net charge of 0.2480 !!! WARNING: PRO 112 has a net charge of 0.1120 !!! WARNING: THR 113 has a net charge of 0.2680 !!! WARNING: GLY 114 has a net charge of 0.2460 !!! WARNING: PHE 115 has a net charge of 0.2140 !!! WARNING: LYS 116 has a net charge of 0.2270 !!! WARNING: PRO 117 has a net charge of 0.1120 !!! WARNING: GLY 118 has a net charge of 0.2460 !!! WARNING: LYS 119 has a net charge of 0.2270 !!! WARNING: GLU 120 has a net charge of 0.2460 !!! WARNING: PHE 121 has a net charge of 0.2140 !!! WARNING: PHE 122 has a net charge of 0.2140 !!! WARNING: PRO 123 has a net charge of 0.1120 !!! WARNING: LEU 124 has a net charge of 0.2040 !!! WARNING: ASP 125 has a net charge of 0.2460 !!! WARNING: GLU 126 has a net charge of 0.2460 !!! WARNING: SER 127 has a net charge of 0.2920 !!! WARNING: GLY 128 has a net charge of 0.2460 !!! WARNING: ASN 129 has a net charge of 0.2170 !!! WARNING: VAL 130 has a net charge of 0.2010 !!! WARNING: VAL 131 has a net charge of 0.2010 !!! WARNING: PRO 132 has a net charge of 0.1120 !!! WARNING: SER 133 has a net charge of 0.2920 !!! WARNING: ASP 134 has a net charge of 0.2460 !!! WARNING: THR 135 has a net charge of 0.2680 !!! WARNING: ASN 136 has a net charge of 0.2170 !!! WARNING: ILE 137 has a net charge of 0.1990 !!! WARNING: LEU 138 has a net charge of 0.2040 !!! WARNING: ASP 139 has a net charge of 0.2460 !!! WARNING: THR 140 has a net charge of 0.2680 !!! WARNING: TRP 141 has a net charge of 0.2480 !!! WARNING: ALA 142 has a net charge of 0.2150 !!! WARNING: ALA 143 has a net charge of 0.2150 !!! WARNING: MET 144 has a net charge of 0.1370 !!! WARNING: GLU 145 has a net charge of 0.2460 !!! WARNING: GLU 146 has a net charge of 0.2460 !!! WARNING: LEU 147 has a net charge of 0.2040 !!! WARNING: VAL 148 has a net charge of 0.2010 !!! WARNING: GLY 151 has a net charge of 0.2460 !!! WARNING: LEU 152 has a net charge of 0.2040 !!! WARNING: VAL 153 has a net charge of 0.2010 !!! WARNING: LYS 154 has a net charge of 0.2270 !!! WARNING: ALA 155 has a net charge of 0.2150 !!! WARNING: ILE 156 has a net charge of 0.1990 !!! WARNING: GLY 157 has a net charge of 0.2460 !!! WARNING: ILE 158 has a net charge of 0.1990 !!! WARNING: SER 159 has a net charge of 0.2920 !!! WARNING: ASN 160 has a net charge of 0.2170 !!! WARNING: PHE 161 has a net charge of 0.2140 !!! WARNING: ASN 162 has a net charge of 0.2170 !!! WARNING: LEU 164 has a net charge of 0.2040 !!! WARNING: GLN 165 has a net charge of 0.2100 !!! WARNING: VAL 166 has a net charge of 0.2010 !!! WARNING: GLU 167 has a net charge of 0.2460 !!! WARNING: MET 168 has a net charge of 0.1370 !!! WARNING: ILE 169 has a net charge of 0.1990 !!! WARNING: LEU 170 has a net charge of 0.2040 !!! WARNING: ASN 171 has a net charge of 0.2170 !!! WARNING: LYS 172 has a net charge of 0.2270 !!! WARNING: PRO 173 has a net charge of 0.1120 !!! WARNING: LEU 175 has a net charge of 0.2040 !!! WARNING: LYS 176 has a net charge of 0.2270 !!! WARNING: TYR 177 has a net charge of 0.2450 !!! WARNING: LYS 178 has a net charge of 0.2270 !!! WARNING: PRO 179 has a net charge of 0.1120 !!! WARNING: ALA 180 has a net charge of 0.2150 !!! WARNING: VAL 181 has a net charge of 0.2010 !!! WARNING: ASN 182 has a net charge of 0.2170 !!! WARNING: GLN 183 has a net charge of 0.2100 !!! WARNING: ILE 184 has a net charge of 0.1990 !!! WARNING: GLU 185 has a net charge of 0.2460 !!! WARNING: CYS 186 has a net charge of 0.1460 !!! WARNING: PRO 188 has a net charge of 0.1120 !!! WARNING: TYR 189 has a net charge of 0.2450 !!! WARNING: LEU 190 has a net charge of 0.2040 !!! WARNING: THR 191 has a net charge of 0.2680 !!! WARNING: GLN 192 has a net charge of 0.2100 !!! WARNING: GLU 193 has a net charge of 0.2460 !!! WARNING: LYS 194 has a net charge of 0.2270 !!! WARNING: LEU 195 has a net charge of 0.2040 !!! WARNING: ILE 196 has a net charge of 0.1990 !!! WARNING: GLN 197 has a net charge of 0.2100 !!! WARNING: TYR 198 has a net charge of 0.2450 !!! WARNING: CYS 199 has a net charge of 0.1460 !!! WARNING: GLN 200 has a net charge of 0.2100 !!! WARNING: SER 201 has a net charge of 0.2920 !!! WARNING: LYS 202 has a net charge of 0.2270 !!! WARNING: GLY 203 has a net charge of 0.2460 !!! WARNING: ILE 204 has a net charge of 0.1990 !!! WARNING: VAL 205 has a net charge of 0.2010 !!! WARNING: VAL 206 has a net charge of 0.2010 !!! WARNING: THR 207 has a net charge of 0.2680 !!! WARNING: ALA 208 has a net charge of 0.2150 !!! WARNING: TYR 209 has a net charge of 0.2450 !!! WARNING: SER 210 has a net charge of 0.2920 !!! WARNING: PRO 211 has a net charge of 0.1120 !!! WARNING: LEU 212 has a net charge of 0.2040 !!! WARNING: GLY 213 has a net charge of 0.2460 !!! WARNING: SER 214 has a net charge of 0.2920 !!! WARNING: PRO 215 has a net charge of 0.1120 !!! WARNING: ASP 216 has a net charge of 0.2460 !!! WARNING: ARG 217 has a net charge of 0.2370 !!! WARNING: PRO 218 has a net charge of 0.1120 !!! WARNING: TRP 219 has a net charge of 0.2480 !!! WARNING: ALA 220 has a net charge of 0.2150 !!! WARNING: LYS 221 has a net charge of 0.2270 !!! WARNING: PRO 222 has a net charge of 0.1120 !!! WARNING: GLU 223 has a net charge of 0.2460 !!! WARNING: ASP 224 has a net charge of 0.2460 !!! WARNING: PRO 225 has a net charge of 0.1120 !!! WARNING: SER 226 has a net charge of 0.2920 !!! WARNING: LEU 227 has a net charge of 0.2040 !!! WARNING: LEU 228 has a net charge of 0.2040 !!! WARNING: GLU 229 has a net charge of 0.2460 !!! WARNING: ASP 230 has a net charge of 0.2460 !!! WARNING: ILE 233 has a net charge of 0.1990 !!! WARNING: THR 243 has a net charge of 0.2680 !!! WARNING: THR 244 has a net charge of 0.2680 !!! WARNING: ALA 245 has a net charge of 0.2150 !!! WARNING: GLN 246 has a net charge of 0.2100 !!! WARNING: VAL 247 has a net charge of 0.2010 !!! WARNING: LEU 248 has a net charge of 0.2040 !!! WARNING: ILE 249 has a net charge of 0.1990 !!! WARNING: ARG 250 has a net charge of 0.2370 !!! WARNING: PHE 251 has a net charge of 0.2140 !!! WARNING: PRO 252 has a net charge of 0.1120 !!! WARNING: MET 253 has a net charge of 0.1370 !!! WARNING: GLN 254 has a net charge of 0.2100 !!! WARNING: ARG 255 has a net charge of 0.2370 !!! WARNING: ASN 256 has a net charge of 0.2170 !!! WARNING: LEU 257 has a net charge of 0.2040 !!! WARNING: VAL 258 has a net charge of 0.2010 !!! WARNING: VAL 259 has a net charge of 0.2010 !!! WARNING: ILE 260 has a net charge of 0.1990 !!! WARNING: PRO 261 has a net charge of 0.1120 !!! WARNING: LYS 262 has a net charge of 0.2270 !!! WARNING: SER 263 has a net charge of 0.2920 !!! WARNING: VAL 264 has a net charge of 0.2010 !!! WARNING: THR 265 has a net charge of 0.2680 !!! WARNING: PRO 266 has a net charge of 0.1120 !!! WARNING: GLU 267 has a net charge of 0.2460 !!! WARNING: ARG 268 has a net charge of 0.2370 !!! WARNING: ILE 269 has a net charge of 0.1990 !!! WARNING: ALA 270 has a net charge of 0.2150 !!! WARNING: GLU 271 has a net charge of 0.2460 !!! WARNING: ASN 272 has a net charge of 0.2170 !!! WARNING: PHE 273 has a net charge of 0.2140 !!! WARNING: LYS 274 has a net charge of 0.2270 !!! WARNING: VAL 275 has a net charge of 0.2010 !!! WARNING: LEU 288 has a net charge of 0.2040 !!! WARNING: LEU 289 has a net charge of 0.2040 !!! WARNING: SER 290 has a net charge of 0.2920 !!! WARNING: TYR 291 has a net charge of 0.2450 !!! WARNING: ASN 292 has a net charge of 0.2170 !!! WARNING: ARG 293 has a net charge of 0.2370 !!! WARNING: ASN 294 has a net charge of 0.2170 !!! WARNING: TRP 295 has a net charge of 0.2480 !!! WARNING: ARG 296 has a net charge of 0.2370 !!! WARNING: VAL 297 has a net charge of 0.2010 !!! WARNING: CYS 298 has a net charge of 0.1460 !!! WARNING: ALA 299 has a net charge of 0.2150 !!! WARNING: LEU 300 has a net charge of 0.2040 !!! WARNING: LEU 301 has a net charge of 0.2040 !!! WARNING: SER 302 has a net charge of 0.2920 !!! WARNING: CYS 303 has a net charge of 0.1460 !!! WARNING: THR 304 has a net charge of 0.2680 !!! WARNING: SER 305 has a net charge of 0.2920 !!! WARNING: LYS 307 has a net charge of 0.2270 !!! WARNING: ASP 308 has a net charge of 0.2460 !!! WARNING: TYR 309 has a net charge of 0.2450 !!! WARNING: PRO 310 has a net charge of 0.1120 !!! WARNING: PHE 311 has a net charge of 0.2140 !!! WARNING: GLU 313 has a net charge of 0.2460 !!! WARNING: GLU 314 has a net charge of 0.2460 !!! WARNING: PHE 315 has a net charge of 0.2140 !!! WARNING: NAP 350 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 2.107132 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): 41.94700 91.94300 ymin,ymax (A): -58.12200 -12.22000 zmin,zma (A): -29.04600 21.63900 x,y,z range (A): 49.99600 45.90200 50.68500 scale (grids/A): 2.107132 object centre (A): 66.94500 -35.17100 -3.703501 number of atom coordinates read : 446 total number of charged atoms : 326 net assigned charge : 58.27298 assigned positive charge : 71.27699 centred at (gu) : 94.54405 94.64385 91.38846 assigned negative charge : -13.00400 centred at (gu) : 105.7525 91.14298 111.7533 start vw surface at 5.0000001E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 49087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20949 grid for indexing accessible points = 1.400000 m= 16199 mr = 18028 m= 5719 mr = 7320 m= 1112 mr = 2661 m= 63 mr = 284 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 43887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 2608 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) : 0.7023774 object centre at (A) : 66.94500 -35.17100 -3.703501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2181860 0.1261295 midg,1,midg; midg,igrid,midg 0.1302280 0.2337909 1,midg,midg; igrid,midg,midg 0.1857269 0.2460145 gauss-seidel spectral radius is 0.9988638 estimated iterations to convergence 235 setup time was (sec) 0.7800000 now iterating at: 13:39:33 rms-change max change #iterations 1.621452 215.9010 at 10iterations 0.7712845 105.7923 at 20iterations 0.3728753 39.85954 at 30iterations 0.1840530 18.93687 at 40iterations 9.0425111E-02 6.854725 at 50iterations 4.4686228E-02 3.877678 at 60iterations 2.2242518E-02 2.099222 at 70iterations 1.1231538E-02 0.7395935 at 80iterations 5.7716994E-03 0.3974724 at 90iterations 3.0600098E-03 0.1734276 at 100iterations 1.6440725E-03 8.4541321E-02 at 110iterations 9.2087837E-04 4.3426514E-02 at 120iterations finished qdiffx linear iterations at : 13:39:44 total time elapsed so far: 12.30000 # loops : 120 mean,max change (kT/e) : 9.2087837E-04 4.3426514E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 13:39:45 12.478u 0.537s 0:13.26 98.0% 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 Sat Oct 8 2011 at 13:39:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 446 !!! WARNING: SER 2 has a net charge of 0.2920 !!! WARNING: ARG 3 has a net charge of 0.2370 !!! WARNING: LEU 4 has a net charge of 0.2040 !!! WARNING: LEU 5 has a net charge of 0.2040 !!! WARNING: LEU 6 has a net charge of 0.2040 !!! WARNING: ASN 7 has a net charge of 0.2170 !!! WARNING: ASN 8 has a net charge of 0.2170 !!! WARNING: ALA 10 has a net charge of 0.2150 !!! WARNING: LYS 11 has a net charge of 0.2270 !!! WARNING: MET 12 has a net charge of 0.1370 !!! WARNING: PRO 13 has a net charge of 0.1120 !!! WARNING: ILE 14 has a net charge of 0.1990 !!! WARNING: LEU 15 has a net charge of 0.2040 !!! WARNING: GLY 16 has a net charge of 0.2460 !!! WARNING: LEU 17 has a net charge of 0.2040 !!! WARNING: GLY 18 has a net charge of 0.2460 !!! WARNING: THR 19 has a net charge of 0.2680 !!! WARNING: TRP 20 has a net charge of 0.2480 !!! WARNING: LYS 21 has a net charge of 0.2270 !!! WARNING: SER 22 has a net charge of 0.2920 !!! WARNING: PRO 23 has a net charge of 0.1120 !!! WARNING: PRO 24 has a net charge of 0.1120 !!! WARNING: GLY 25 has a net charge of 0.2460 !!! WARNING: GLN 26 has a net charge of 0.2100 !!! WARNING: VAL 27 has a net charge of 0.2010 !!! WARNING: THR 28 has a net charge of 0.2680 !!! WARNING: GLU 29 has a net charge of 0.2460 !!! WARNING: ALA 30 has a net charge of 0.2150 !!! WARNING: VAL 31 has a net charge of 0.2010 !!! WARNING: LYS 32 has a net charge of 0.2270 !!! WARNING: VAL 33 has a net charge of 0.2010 !!! WARNING: ALA 34 has a net charge of 0.2150 !!! WARNING: ILE 35 has a net charge of 0.1990 !!! WARNING: VAL 37 has a net charge of 0.2010 !!! WARNING: GLY 38 has a net charge of 0.2460 !!! WARNING: TYR 39 has a net charge of 0.2450 !!! WARNING: ARG 40 has a net charge of 0.2370 !!! WARNING: ILE 42 has a net charge of 0.1990 !!! WARNING: ASP 43 has a net charge of 0.2460 !!! WARNING: CYS 44 has a net charge of 0.1460 !!! WARNING: ALA 45 has a net charge of 0.2150 !!! WARNING: VAL 47 has a net charge of 0.2010 !!! WARNING: TYR 48 has a net charge of 0.2450 !!! WARNING: GLN 49 has a net charge of 0.2100 !!! WARNING: ASN 50 has a net charge of 0.2170 !!! WARNING: GLU 51 has a net charge of 0.2460 !!! WARNING: ASN 52 has a net charge of 0.2170 !!! WARNING: GLU 53 has a net charge of 0.2460 !!! WARNING: VAL 54 has a net charge of 0.2010 !!! WARNING: GLY 55 has a net charge of 0.2460 !!! WARNING: VAL 56 has a net charge of 0.2010 !!! WARNING: ALA 57 has a net charge of 0.2150 !!! WARNING: ILE 58 has a net charge of 0.1990 !!! WARNING: GLN 59 has a net charge of 0.2100 !!! WARNING: GLU 60 has a net charge of 0.2460 !!! WARNING: ARG 69 has a net charge of 0.2370 !!! WARNING: GLU 70 has a net charge of 0.2460 !!! WARNING: GLU 71 has a net charge of 0.2460 !!! WARNING: LEU 72 has a net charge of 0.2040 !!! WARNING: PHE 73 has a net charge of 0.2140 !!! WARNING: ILE 74 has a net charge of 0.1990 !!! WARNING: VAL 75 has a net charge of 0.2010 !!! WARNING: SER 76 has a net charge of 0.2920 !!! WARNING: LYS 77 has a net charge of 0.2270 !!! WARNING: LEU 78 has a net charge of 0.2040 !!! WARNING: TRP 79 has a net charge of 0.2480 !!! WARNING: CYS 80 has a net charge of 0.1460 !!! WARNING: THR 81 has a net charge of 0.2680 !!! WARNING: TYR 82 has a net charge of 0.2450 !!! WARNING: GLU 84 has a net charge of 0.2460 !!! WARNING: LYS 85 has a net charge of 0.2270 !!! WARNING: GLY 86 has a net charge of 0.2460 !!! WARNING: LEU 87 has a net charge of 0.2040 !!! WARNING: VAL 88 has a net charge of 0.2010 !!! WARNING: LYS 89 has a net charge of 0.2270 !!! WARNING: GLY 90 has a net charge of 0.2460 !!! WARNING: ALA 91 has a net charge of 0.2150 !!! WARNING: CYS 92 has a net charge of 0.1460 !!! WARNING: GLN 93 has a net charge of 0.2100 !!! WARNING: LYS 94 has a net charge of 0.2270 !!! WARNING: THR 95 has a net charge of 0.2680 !!! WARNING: LEU 96 has a net charge of 0.2040 !!! WARNING: SER 97 has a net charge of 0.2920 !!! WARNING: ASP 98 has a net charge of 0.2460 !!! WARNING: LEU 99 has a net charge of 0.2040 !!! WARNING: LYS 100 has a net charge of 0.2270 !!! WARNING: LEU 101 has a net charge of 0.2040 !!! WARNING: ASP 102 has a net charge of 0.2460 !!! WARNING: TYR 103 has a net charge of 0.2450 !!! WARNING: LEU 104 has a net charge of 0.2040 !!! WARNING: ASP 105 has a net charge of 0.2460 !!! WARNING: LEU 106 has a net charge of 0.2040 !!! WARNING: TYR 107 has a net charge of 0.2450 !!! WARNING: LEU 108 has a net charge of 0.2040 !!! WARNING: ILE 109 has a net charge of 0.1990 !!! WARNING: TRP 111 has a net charge of 0.2480 !!! WARNING: PRO 112 has a net charge of 0.1120 !!! WARNING: THR 113 has a net charge of 0.2680 !!! WARNING: GLY 114 has a net charge of 0.2460 !!! WARNING: PHE 115 has a net charge of 0.2140 !!! WARNING: LYS 116 has a net charge of 0.2270 !!! WARNING: PRO 117 has a net charge of 0.1120 !!! WARNING: GLY 118 has a net charge of 0.2460 !!! WARNING: LYS 119 has a net charge of 0.2270 !!! WARNING: GLU 120 has a net charge of 0.2460 !!! WARNING: PHE 121 has a net charge of 0.2140 !!! WARNING: PHE 122 has a net charge of 0.2140 !!! WARNING: PRO 123 has a net charge of 0.1120 !!! WARNING: LEU 124 has a net charge of 0.2040 !!! WARNING: ASP 125 has a net charge of 0.2460 !!! WARNING: GLU 126 has a net charge of 0.2460 !!! WARNING: SER 127 has a net charge of 0.2920 !!! WARNING: GLY 128 has a net charge of 0.2460 !!! WARNING: ASN 129 has a net charge of 0.2170 !!! WARNING: VAL 130 has a net charge of 0.2010 !!! WARNING: VAL 131 has a net charge of 0.2010 !!! WARNING: PRO 132 has a net charge of 0.1120 !!! WARNING: SER 133 has a net charge of 0.2920 !!! WARNING: ASP 134 has a net charge of 0.2460 !!! WARNING: THR 135 has a net charge of 0.2680 !!! WARNING: ASN 136 has a net charge of 0.2170 !!! WARNING: ILE 137 has a net charge of 0.1990 !!! WARNING: LEU 138 has a net charge of 0.2040 !!! WARNING: ASP 139 has a net charge of 0.2460 !!! WARNING: THR 140 has a net charge of 0.2680 !!! WARNING: TRP 141 has a net charge of 0.2480 !!! WARNING: ALA 142 has a net charge of 0.2150 !!! WARNING: ALA 143 has a net charge of 0.2150 !!! WARNING: MET 144 has a net charge of 0.1370 !!! WARNING: GLU 145 has a net charge of 0.2460 !!! WARNING: GLU 146 has a net charge of 0.2460 !!! WARNING: LEU 147 has a net charge of 0.2040 !!! WARNING: VAL 148 has a net charge of 0.2010 !!! WARNING: GLY 151 has a net charge of 0.2460 !!! WARNING: LEU 152 has a net charge of 0.2040 !!! WARNING: VAL 153 has a net charge of 0.2010 !!! WARNING: LYS 154 has a net charge of 0.2270 !!! WARNING: ALA 155 has a net charge of 0.2150 !!! WARNING: ILE 156 has a net charge of 0.1990 !!! WARNING: GLY 157 has a net charge of 0.2460 !!! WARNING: ILE 158 has a net charge of 0.1990 !!! WARNING: SER 159 has a net charge of 0.2920 !!! WARNING: ASN 160 has a net charge of 0.2170 !!! WARNING: PHE 161 has a net charge of 0.2140 !!! WARNING: ASN 162 has a net charge of 0.2170 !!! WARNING: LEU 164 has a net charge of 0.2040 !!! WARNING: GLN 165 has a net charge of 0.2100 !!! WARNING: VAL 166 has a net charge of 0.2010 !!! WARNING: GLU 167 has a net charge of 0.2460 !!! WARNING: MET 168 has a net charge of 0.1370 !!! WARNING: ILE 169 has a net charge of 0.1990 !!! WARNING: LEU 170 has a net charge of 0.2040 !!! WARNING: ASN 171 has a net charge of 0.2170 !!! WARNING: LYS 172 has a net charge of 0.2270 !!! WARNING: PRO 173 has a net charge of 0.1120 !!! WARNING: LEU 175 has a net charge of 0.2040 !!! WARNING: LYS 176 has a net charge of 0.2270 !!! WARNING: TYR 177 has a net charge of 0.2450 !!! WARNING: LYS 178 has a net charge of 0.2270 !!! WARNING: PRO 179 has a net charge of 0.1120 !!! WARNING: ALA 180 has a net charge of 0.2150 !!! WARNING: VAL 181 has a net charge of 0.2010 !!! WARNING: ASN 182 has a net charge of 0.2170 !!! WARNING: GLN 183 has a net charge of 0.2100 !!! WARNING: ILE 184 has a net charge of 0.1990 !!! WARNING: GLU 185 has a net charge of 0.2460 !!! WARNING: CYS 186 has a net charge of 0.1460 !!! WARNING: PRO 188 has a net charge of 0.1120 !!! WARNING: TYR 189 has a net charge of 0.2450 !!! WARNING: LEU 190 has a net charge of 0.2040 !!! WARNING: THR 191 has a net charge of 0.2680 !!! WARNING: GLN 192 has a net charge of 0.2100 !!! WARNING: GLU 193 has a net charge of 0.2460 !!! WARNING: LYS 194 has a net charge of 0.2270 !!! WARNING: LEU 195 has a net charge of 0.2040 !!! WARNING: ILE 196 has a net charge of 0.1990 !!! WARNING: GLN 197 has a net charge of 0.2100 !!! WARNING: TYR 198 has a net charge of 0.2450 !!! WARNING: CYS 199 has a net charge of 0.1460 !!! WARNING: GLN 200 has a net charge of 0.2100 !!! WARNING: SER 201 has a net charge of 0.2920 !!! WARNING: LYS 202 has a net charge of 0.2270 !!! WARNING: GLY 203 has a net charge of 0.2460 !!! WARNING: ILE 204 has a net charge of 0.1990 !!! WARNING: VAL 205 has a net charge of 0.2010 !!! WARNING: VAL 206 has a net charge of 0.2010 !!! WARNING: THR 207 has a net charge of 0.2680 !!! WARNING: ALA 208 has a net charge of 0.2150 !!! WARNING: TYR 209 has a net charge of 0.2450 !!! WARNING: SER 210 has a net charge of 0.2920 !!! WARNING: PRO 211 has a net charge of 0.1120 !!! WARNING: LEU 212 has a net charge of 0.2040 !!! WARNING: GLY 213 has a net charge of 0.2460 !!! WARNING: SER 214 has a net charge of 0.2920 !!! WARNING: PRO 215 has a net charge of 0.1120 !!! WARNING: ASP 216 has a net charge of 0.2460 !!! WARNING: ARG 217 has a net charge of 0.2370 !!! WARNING: PRO 218 has a net charge of 0.1120 !!! WARNING: TRP 219 has a net charge of 0.2480 !!! WARNING: ALA 220 has a net charge of 0.2150 !!! WARNING: LYS 221 has a net charge of 0.2270 !!! WARNING: PRO 222 has a net charge of 0.1120 !!! WARNING: GLU 223 has a net charge of 0.2460 !!! WARNING: ASP 224 has a net charge of 0.2460 !!! WARNING: PRO 225 has a net charge of 0.1120 !!! WARNING: SER 226 has a net charge of 0.2920 !!! WARNING: LEU 227 has a net charge of 0.2040 !!! WARNING: LEU 228 has a net charge of 0.2040 !!! WARNING: GLU 229 has a net charge of 0.2460 !!! WARNING: ASP 230 has a net charge of 0.2460 !!! WARNING: ILE 233 has a net charge of 0.1990 !!! WARNING: THR 243 has a net charge of 0.2680 !!! WARNING: THR 244 has a net charge of 0.2680 !!! WARNING: ALA 245 has a net charge of 0.2150 !!! WARNING: GLN 246 has a net charge of 0.2100 !!! WARNING: VAL 247 has a net charge of 0.2010 !!! WARNING: LEU 248 has a net charge of 0.2040 !!! WARNING: ILE 249 has a net charge of 0.1990 !!! WARNING: ARG 250 has a net charge of 0.2370 !!! WARNING: PHE 251 has a net charge of 0.2140 !!! WARNING: PRO 252 has a net charge of 0.1120 !!! WARNING: MET 253 has a net charge of 0.1370 !!! WARNING: GLN 254 has a net charge of 0.2100 !!! WARNING: ARG 255 has a net charge of 0.2370 !!! WARNING: ASN 256 has a net charge of 0.2170 !!! WARNING: LEU 257 has a net charge of 0.2040 !!! WARNING: VAL 258 has a net charge of 0.2010 !!! WARNING: VAL 259 has a net charge of 0.2010 !!! WARNING: ILE 260 has a net charge of 0.1990 !!! WARNING: PRO 261 has a net charge of 0.1120 !!! WARNING: LYS 262 has a net charge of 0.2270 !!! WARNING: SER 263 has a net charge of 0.2920 !!! WARNING: VAL 264 has a net charge of 0.2010 !!! WARNING: THR 265 has a net charge of 0.2680 !!! WARNING: PRO 266 has a net charge of 0.1120 !!! WARNING: GLU 267 has a net charge of 0.2460 !!! WARNING: ARG 268 has a net charge of 0.2370 !!! WARNING: ILE 269 has a net charge of 0.1990 !!! WARNING: ALA 270 has a net charge of 0.2150 !!! WARNING: GLU 271 has a net charge of 0.2460 !!! WARNING: ASN 272 has a net charge of 0.2170 !!! WARNING: PHE 273 has a net charge of 0.2140 !!! WARNING: LYS 274 has a net charge of 0.2270 !!! WARNING: VAL 275 has a net charge of 0.2010 !!! WARNING: LEU 288 has a net charge of 0.2040 !!! WARNING: LEU 289 has a net charge of 0.2040 !!! WARNING: SER 290 has a net charge of 0.2920 !!! WARNING: TYR 291 has a net charge of 0.2450 !!! WARNING: ASN 292 has a net charge of 0.2170 !!! WARNING: ARG 293 has a net charge of 0.2370 !!! WARNING: ASN 294 has a net charge of 0.2170 !!! WARNING: TRP 295 has a net charge of 0.2480 !!! WARNING: ARG 296 has a net charge of 0.2370 !!! WARNING: VAL 297 has a net charge of 0.2010 !!! WARNING: CYS 298 has a net charge of 0.1460 !!! WARNING: ALA 299 has a net charge of 0.2150 !!! WARNING: LEU 300 has a net charge of 0.2040 !!! WARNING: LEU 301 has a net charge of 0.2040 !!! WARNING: SER 302 has a net charge of 0.2920 !!! WARNING: CYS 303 has a net charge of 0.1460 !!! WARNING: THR 304 has a net charge of 0.2680 !!! WARNING: SER 305 has a net charge of 0.2920 !!! WARNING: LYS 307 has a net charge of 0.2270 !!! WARNING: ASP 308 has a net charge of 0.2460 !!! WARNING: TYR 309 has a net charge of 0.2450 !!! WARNING: PRO 310 has a net charge of 0.1120 !!! WARNING: PHE 311 has a net charge of 0.2140 !!! WARNING: GLU 313 has a net charge of 0.2460 !!! WARNING: GLU 314 has a net charge of 0.2460 !!! WARNING: PHE 315 has a net charge of 0.2140 !!! WARNING: NAP 350 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 3.160698 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): 41.94700 91.94300 ymin,ymax (A): -58.12200 -12.22000 zmin,zma (A): -29.04600 21.63900 x,y,z range (A): 49.99600 45.90200 50.68500 scale (grids/A): 3.160698 object centre (A): 66.94500 -35.17100 -3.703501 number of atom coordinates read : 446 total number of charged atoms : 326 net assigned charge : 58.27298 assigned positive charge : 71.27699 centred at (gu) : 96.81615 96.96572 92.08267 assigned negative charge : -13.00400 centred at (gu) : 113.6288 91.71447 122.6300 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 111635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20949 grid for indexing accessible points = 1.400000 m= 44938 mr = 46934 m= 22106 mr = 26046 m= 10889 mr = 13096 m= 3567 mr = 6578 m= 483 mr = 1800 m= 25 mr = 149 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 99040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 2608 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) : 2.107132 object centre at (A) : 66.94500 -35.17100 -3.703501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.877657 1.044443 midg,1,midg; midg,igrid,midg 1.097154 1.888520 1,midg,midg; igrid,midg,midg 1.565926 2.148871 gauss-seidel spectral radius is 0.9994130 estimated iterations to convergence 325 setup time was (sec) 1.480000 now iterating at: 13:39:47 rms-change max change #iterations 3.839266 342.0341 at 10iterations 2.462859 137.0361 at 20iterations 1.533674 80.10396 at 30iterations 0.9587954 53.05632 at 40iterations 0.5978469 27.59674 at 50iterations 0.3674446 15.88416 at 60iterations 0.2253061 12.24110 at 70iterations 0.1376851 5.713028 at 80iterations 8.3533213E-02 3.504635 at 90iterations 5.0858036E-02 1.781655 at 100iterations 3.1027872E-02 1.223841 at 110iterations 1.8931506E-02 0.6505585 at 120iterations 1.1474555E-02 0.4080162 at 130iterations 7.0056426E-03 0.2248192 at 140iterations 4.2727403E-03 0.1402817 at 150iterations 2.6225871E-03 7.8664780E-02 at 160iterations 1.5948761E-03 5.5934906E-02 at 170iterations 9.8532427E-04 2.7088165E-02 at 180iterations finished qdiffx linear iterations at : 13:40:07 total time elapsed so far: 21.36000 # loops : 180 mean,max change (kT/e) : 9.8532427E-04 2.7088165E-02 energy calculations done at 21.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.53000 DelPhi exited at 13:40:07 21.537u 0.566s 0:22.45 98.3% 0+0k 0+0io 0pf+0w