Thu Jan 19 13:33:33 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.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 Thu Jan 19 2012 at 13:33:36 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: ASN 2 has a net charge of -0.6880 !!! WARNING: ASN 7 has a net charge of -0.6880 !!! WARNING: GLN 10 has a net charge of -0.6880 !!! WARNING: ASN 11 has a net charge of -0.6880 !!! WARNING: ARG 12 has a net charge of -0.4460 !!! WARNING: GLN 22 has a net charge of -0.4400 !!! WARNING: ARG 29 has a net charge of -0.4460 !!! WARNING: ASN 36 has a net charge of -0.6880 !!! WARNING: ARG 45 has a net charge of -0.4460 !!! WARNING: ASN 55 has a net charge of -0.6880 !!! WARNING: ASN 69 has a net charge of -0.6880 !!! WARNING: ASN 72 has a net charge of -0.6880 !!! WARNING: ASN 73 has a net charge of -0.6880 !!! WARNING: ARG 78 has a net charge of -0.4460 !!! WARNING: ARG 89 has a net charge of -0.4460 !!! WARNING: ASN 100 has a net charge of -0.6880 !!! WARNING: ASN 113 has a net charge of -0.6880 !!! WARNING: ARG 119 has a net charge of -0.4460 !!! WARNING: ASN 137 has a net charge of -0.6880 !!! WARNING: ARG 153 has a net charge of -0.4460 !!! WARNING: ARG 154 has a net charge of -0.4460 !!! WARNING: GLN 161 has a net charge of -0.6880 !!! WARNING: ASN 164 has a net charge of -0.6880 !!! WARNING: GLN 172 has a net charge of -0.6880 !!! WARNING: GLN 177 has a net charge of -0.6880 !!! WARNING: ARG 185 has a net charge of -0.4460 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 200 has a net charge of -0.6880 !!! WARNING: ARG 209 has a net charge of -0.4460 !!! WARNING: GLN 210 has a net charge of -0.6880 !!! WARNING: ARG 214 has a net charge of -0.4460 !!! WARNING: GLN 224 has a net charge of -0.6880 !!! WARNING: GLY 228 has a net charge of 0.2480 !!! WARNING: THR 238 has a net charge of 0.2480 !!! WARNING: GLN 239 has a net charge of -0.6880 !!! WARNING: ASN 251 has a net charge of -0.9360 !!! WARNING: GLN 253 has a net charge of -0.6880 !!! WARNING: GLN 258 has a net charge of -0.6880 !!! WARNING: ARG 276 has a net charge of -0.4460 !!! WARNING: GLN 279 has a net charge of -0.6880 !!! WARNING: ARG 280 has a net charge of -0.4460 !!! WARNING: GLN 287 has a net charge of -0.6880 !!! WARNING: TRP 292 has a net charge of 0.2480 !!! WARNING: ASP 294 has a net charge of -0.7520 !!! WARNING: GLN 296 has a net charge of -0.6880 !!! WARNING: GLN 299 has a net charge of -0.6880 !!! WARNING: GLN 319 has a net charge of -0.6880 !!! WARNING: ASN 337 has a net charge of -0.6880 !!! WARNING: GLN 338 has a net charge of -0.6880 !!! WARNING: GLN 339 has a net charge of -0.6880 !!! WARNING: GLN 341 has a net charge of -0.6880 !!! WARNING: GLN 343 has a net charge of -0.6880 !!! WARNING: ASN 344 has a net charge of -0.6880 !!! WARNING: ARG 345 has a net charge of -0.4460 !!! WARNING: ASN 351 has a net charge of -0.6880 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ASN 365 has a net charge of -0.6880 !!! WARNING: GLN 369 has a net charge of -0.6880 !!! WARNING: GLN 375 has a net charge of -0.6880 !!! WARNING: ASN 379 has a net charge of -0.6880 !!! WARNING: ASN 380 has a net charge of -0.6880 !!! WARNING: GLN 390 has a net charge of -0.6880 !!! WARNING: ARG 397 has a net charge of -0.4460 !!! WARNING: GLN 398 has a net charge of -0.6880 !!! WARNING: ARG 402 has a net charge of -0.4460 !!! WARNING: ARG 407 has a net charge of -0.4460 !!! WARNING: ASN 408 has a net charge of -0.6880 !!! WARNING: GLN 414 has a net charge of -0.6880 !!! WARNING: GLN 423 has a net charge of -0.6880 !!! WARNING: ARG 425 has a net charge of -0.4460 !!! WARNING: GLN 430 has a net charge of -0.6880 !!! WARNING: ASN 433 has a net charge of -0.6880 !!! WARNING: ARG 436 has a net charge of -0.4460 !!! WARNING: ARG 438 has a net charge of -0.4460 !!! WARNING: ARG 482 has a net charge of -0.4460 !!! WARNING: ASN 506 has a net charge of -0.6880 !!! WARNING: GLN 512 has a net charge of -0.6880 !!! WARNING: ASN 529 has a net charge of -0.6880 !!! WARNING: GLN 534 has a net charge of -0.6880 !!! WARNING: ASN 539 has a net charge of -0.6880 !!! WARNING: ASN 540 has a net charge of -0.6880 !!! WARNING: ASN 550 has a net charge of -0.6880 !!! WARNING: GLN 552 has a net charge of -0.6880 !!! WARNING: ASN 563 has a net charge of -0.4400 !!! WARNING: ARG 564 has a net charge of -0.4460 !!! WARNING: LYS 576 has a net charge of 1.2480 !!! WARNING: ARG 581 has a net charge of -0.4460 !!! WARNING: CYX 589 has a net charge of 0.2480 !!! WARNING: GLU 593 has a net charge of -0.7520 !!! WARNING: LEU 595 has a net charge of 0.2480 !!! WARNING: LYS 599 has a net charge of 1.2480 !!! WARNING: LEU 632 has a net charge of 0.2480 !!! WARNING: LYS 635 has a net charge of 1.2480 !!! WARNING: ARG 641 has a net charge of -0.4460 !!! WARNING: ASN 652 has a net charge of -0.6880 !!! WARNING: TYR 655 has a net charge of 0.2480 !!! WARNING: ASN 665 has a net charge of -0.6880 !!! WARNING: ARG 671 has a net charge of -0.4460 !!! WARNING: ARG 737 has a net charge of -0.1980 !!! WARNING: THR 742 has a net charge of 0.2480 !!! WARNING: GLY 744 has a net charge of 0.2480 !!! WARNING: GLU 757 has a net charge of -0.7520 !!! WARNING: GLN 762 has a net charge of -0.4400 !!! WARNING: ARG 766 has a net charge of -0.1980 !!! WARNING: TRP 844 has a net charge of 0.2480 !!! WARNING: GLU 847 has a net charge of -0.7520 !!! WARNING: GLN 848 has a net charge of -0.6880 !!! WARNING: PHE 850 has a net charge of 0.2480 !!! WARNING: GLN 851 has a net charge of -0.6880 !!! WARNING: LYS 854 has a net charge of 1.2480 !!! WARNING: ILE 858 has a net charge of 0.2480 !!! WARNING: ILE 862 has a net charge of 0.2480 !!! WARNING: PHE 882 has a net charge of 0.2480 !!! WARNING: ASN 889 has a net charge of -0.6880 !!! WARNING: GLN 890 has a net charge of -0.6880 !!! WARNING: GLN 891 has a net charge of -0.6880 !!! WARNING: GLN 893 has a net charge of -0.6880 !!! WARNING: GLN 895 has a net charge of -0.6880 !!! WARNING: ASN 896 has a net charge of -0.6880 !!! WARNING: ARG 897 has a net charge of -0.4460 !!! WARNING: ARG 990 has a net charge of -0.1980 !!! WARNING: LEU 1052 has a net charge of 0.2480 !!! WARNING: ASN 1058 has a net charge of -0.6880 !!! WARNING: GLN 1064 has a net charge of -0.6880 !!! WARNING: PHE 1077 has a net charge of 0.2480 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4340193 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): -2.752000 79.27200 ymin,ymax (A): -14.05600 65.52900 zmin,zma (A): -24.43500 42.42700 x,y,z range (A): 82.02400 79.58500 66.86200 scale (grids/A): 0.4340193 object centre (A): 38.26000 25.73650 8.996001 number of atom coordinates read : 6895 total number of charged atoms : 6463 net assigned charge : -82.14730 assigned positive charge : 963.3899 centred at (gu) : 88.15070 90.64165 89.98100 assigned negative charge : -1045.547 centred at (gu) : 88.04163 90.72836 89.90273 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7451 nv = 96 ne = 84 npr = 139694 no. pairs analyzed = 139694 no. exposed pairs = 8823 no. arc points = 60096 no. surface atoms = 2947 nbur = 3948 mkacc time = 0.2400000 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 = 1.932000 m= 192 mr = 3459 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4950 ## 974 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10383 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7384796E-11 -1.4577313E-11 midg,1,midg; midg,igrid,midg -1.1605659E-11 -3.3917851E-11 1,midg,midg; igrid,midg,midg -5.2426619E-11 -7.1959717E-12 gauss-seidel spectral radius is 0.9730598 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 13:33:37 rms-change max change #iterations 5.1807106E-02 7.662426 at 10iterations 1.3232733E-02 1.833260 at 20iterations 5.2045085E-03 0.7720108 at 30iterations 2.0736437E-03 0.3136215 at 40iterations 8.2791853E-04 0.1259384 at 50iterations finished qdiffx linear iterations at : 13:33:45 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 8.2791853E-04 0.1259384 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 13:33:46 3.750u 0.167s 0:09.81 39.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Jan 19 2012 at 13:33:46 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: ASN 2 has a net charge of -0.6880 !!! WARNING: ASN 7 has a net charge of -0.6880 !!! WARNING: GLN 10 has a net charge of -0.6880 !!! WARNING: ASN 11 has a net charge of -0.6880 !!! WARNING: ARG 12 has a net charge of -0.4460 !!! WARNING: GLN 22 has a net charge of -0.4400 !!! WARNING: ARG 29 has a net charge of -0.4460 !!! WARNING: ASN 36 has a net charge of -0.6880 !!! WARNING: ARG 45 has a net charge of -0.4460 !!! WARNING: ASN 55 has a net charge of -0.6880 !!! WARNING: ASN 69 has a net charge of -0.6880 !!! WARNING: ASN 72 has a net charge of -0.6880 !!! WARNING: ASN 73 has a net charge of -0.6880 !!! WARNING: ARG 78 has a net charge of -0.4460 !!! WARNING: ARG 89 has a net charge of -0.4460 !!! WARNING: ASN 100 has a net charge of -0.6880 !!! WARNING: ASN 113 has a net charge of -0.6880 !!! WARNING: ARG 119 has a net charge of -0.4460 !!! WARNING: ASN 137 has a net charge of -0.6880 !!! WARNING: ARG 153 has a net charge of -0.4460 !!! WARNING: ARG 154 has a net charge of -0.4460 !!! WARNING: GLN 161 has a net charge of -0.6880 !!! WARNING: ASN 164 has a net charge of -0.6880 !!! WARNING: GLN 172 has a net charge of -0.6880 !!! WARNING: GLN 177 has a net charge of -0.6880 !!! WARNING: ARG 185 has a net charge of -0.4460 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 200 has a net charge of -0.6880 !!! WARNING: ARG 209 has a net charge of -0.4460 !!! WARNING: GLN 210 has a net charge of -0.6880 !!! WARNING: ARG 214 has a net charge of -0.4460 !!! WARNING: GLN 224 has a net charge of -0.6880 !!! WARNING: GLY 228 has a net charge of 0.2480 !!! WARNING: THR 238 has a net charge of 0.2480 !!! WARNING: GLN 239 has a net charge of -0.6880 !!! WARNING: ASN 251 has a net charge of -0.9360 !!! WARNING: GLN 253 has a net charge of -0.6880 !!! WARNING: GLN 258 has a net charge of -0.6880 !!! WARNING: ARG 276 has a net charge of -0.4460 !!! WARNING: GLN 279 has a net charge of -0.6880 !!! WARNING: ARG 280 has a net charge of -0.4460 !!! WARNING: GLN 287 has a net charge of -0.6880 !!! WARNING: TRP 292 has a net charge of 0.2480 !!! WARNING: ASP 294 has a net charge of -0.7520 !!! WARNING: GLN 296 has a net charge of -0.6880 !!! WARNING: GLN 299 has a net charge of -0.6880 !!! WARNING: GLN 319 has a net charge of -0.6880 !!! WARNING: ASN 337 has a net charge of -0.6880 !!! WARNING: GLN 338 has a net charge of -0.6880 !!! WARNING: GLN 339 has a net charge of -0.6880 !!! WARNING: GLN 341 has a net charge of -0.6880 !!! WARNING: GLN 343 has a net charge of -0.6880 !!! WARNING: ASN 344 has a net charge of -0.6880 !!! WARNING: ARG 345 has a net charge of -0.4460 !!! WARNING: ASN 351 has a net charge of -0.6880 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ASN 365 has a net charge of -0.6880 !!! WARNING: GLN 369 has a net charge of -0.6880 !!! WARNING: GLN 375 has a net charge of -0.6880 !!! WARNING: ASN 379 has a net charge of -0.6880 !!! WARNING: ASN 380 has a net charge of -0.6880 !!! WARNING: GLN 390 has a net charge of -0.6880 !!! WARNING: ARG 397 has a net charge of -0.4460 !!! WARNING: GLN 398 has a net charge of -0.6880 !!! WARNING: ARG 402 has a net charge of -0.4460 !!! WARNING: ARG 407 has a net charge of -0.4460 !!! WARNING: ASN 408 has a net charge of -0.6880 !!! WARNING: GLN 414 has a net charge of -0.6880 !!! WARNING: GLN 423 has a net charge of -0.6880 !!! WARNING: ARG 425 has a net charge of -0.4460 !!! WARNING: GLN 430 has a net charge of -0.6880 !!! WARNING: ASN 433 has a net charge of -0.6880 !!! WARNING: ARG 436 has a net charge of -0.4460 !!! WARNING: ARG 438 has a net charge of -0.4460 !!! WARNING: ARG 482 has a net charge of -0.4460 !!! WARNING: ASN 506 has a net charge of -0.6880 !!! WARNING: GLN 512 has a net charge of -0.6880 !!! WARNING: ASN 529 has a net charge of -0.6880 !!! WARNING: GLN 534 has a net charge of -0.6880 !!! WARNING: ASN 539 has a net charge of -0.6880 !!! WARNING: ASN 540 has a net charge of -0.6880 !!! WARNING: ASN 550 has a net charge of -0.6880 !!! WARNING: GLN 552 has a net charge of -0.6880 !!! WARNING: ASN 563 has a net charge of -0.4400 !!! WARNING: ARG 564 has a net charge of -0.4460 !!! WARNING: LYS 576 has a net charge of 1.2480 !!! WARNING: ARG 581 has a net charge of -0.4460 !!! WARNING: CYX 589 has a net charge of 0.2480 !!! WARNING: GLU 593 has a net charge of -0.7520 !!! WARNING: LEU 595 has a net charge of 0.2480 !!! WARNING: LYS 599 has a net charge of 1.2480 !!! WARNING: LEU 632 has a net charge of 0.2480 !!! WARNING: LYS 635 has a net charge of 1.2480 !!! WARNING: ARG 641 has a net charge of -0.4460 !!! WARNING: ASN 652 has a net charge of -0.6880 !!! WARNING: TYR 655 has a net charge of 0.2480 !!! WARNING: ASN 665 has a net charge of -0.6880 !!! WARNING: ARG 671 has a net charge of -0.4460 !!! WARNING: ARG 737 has a net charge of -0.1980 !!! WARNING: THR 742 has a net charge of 0.2480 !!! WARNING: GLY 744 has a net charge of 0.2480 !!! WARNING: GLU 757 has a net charge of -0.7520 !!! WARNING: GLN 762 has a net charge of -0.4400 !!! WARNING: ARG 766 has a net charge of -0.1980 !!! WARNING: TRP 844 has a net charge of 0.2480 !!! WARNING: GLU 847 has a net charge of -0.7520 !!! WARNING: GLN 848 has a net charge of -0.6880 !!! WARNING: PHE 850 has a net charge of 0.2480 !!! WARNING: GLN 851 has a net charge of -0.6880 !!! WARNING: LYS 854 has a net charge of 1.2480 !!! WARNING: ILE 858 has a net charge of 0.2480 !!! WARNING: ILE 862 has a net charge of 0.2480 !!! WARNING: PHE 882 has a net charge of 0.2480 !!! WARNING: ASN 889 has a net charge of -0.6880 !!! WARNING: GLN 890 has a net charge of -0.6880 !!! WARNING: GLN 891 has a net charge of -0.6880 !!! WARNING: GLN 893 has a net charge of -0.6880 !!! WARNING: GLN 895 has a net charge of -0.6880 !!! WARNING: ASN 896 has a net charge of -0.6880 !!! WARNING: ARG 897 has a net charge of -0.4460 !!! WARNING: ARG 990 has a net charge of -0.1980 !!! WARNING: LEU 1052 has a net charge of 0.2480 !!! WARNING: ASN 1058 has a net charge of -0.6880 !!! WARNING: GLN 1064 has a net charge of -0.6880 !!! WARNING: PHE 1077 has a net charge of 0.2480 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.302058 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): -2.752000 79.27200 ymin,ymax (A): -14.05600 65.52900 zmin,zma (A): -24.43500 42.42700 x,y,z range (A): 82.02400 79.58500 66.86200 scale (grids/A): 1.302058 object centre (A): 38.26000 25.73650 8.996001 number of atom coordinates read : 6895 total number of charged atoms : 6463 net assigned charge : -82.14730 assigned positive charge : 963.3899 centred at (gu) : 84.45005 91.92252 89.94090 assigned negative charge : -1045.547 centred at (gu) : 84.12429 92.18471 89.70746 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 86536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 19736 mr = 56149 m= 929 mr = 11455 m= 11 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4700000 number of dielectric boundary points 39422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 834 ## 23 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 45295 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) : 0.4340193 object centre at (A) : 38.26000 25.73650 8.996001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6496830E-02 -9.2131570E-03 midg,1,midg; midg,igrid,midg -1.4790964E-02 -1.8735379E-02 1,midg,midg; igrid,midg,midg -5.7729576E-02 -1.1028961E-02 gauss-seidel spectral radius is 0.9974630 estimated iterations to convergence 158 setup time was (sec) 0.7200000 now iterating at: 13:33:47 rms-change max change #iterations 3.200064 131.9256 at 10iterations 1.136447 44.45524 at 20iterations 0.4097959 14.07166 at 30iterations 0.1498524 5.189934 at 40iterations 5.6675412E-02 2.066734 at 50iterations 2.4743669E-02 0.8897362 at 60iterations 1.3470555E-02 0.4457703 at 70iterations 8.5718362E-03 0.3033295 at 80iterations 5.9117828E-03 0.1950607 at 90iterations 4.1788905E-03 0.1373138 at 100iterations 2.9638263E-03 9.7778320E-02 at 110iterations 2.1051180E-03 6.9869995E-02 at 120iterations finished qdiffx linear iterations at : 13:34:06 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 2.1051180E-03 6.9869995E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 13:34:07 8.471u 0.231s 0:21.27 40.9% 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 Thu Jan 19 2012 at 13:34:09 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: ASN 2 has a net charge of -0.6880 !!! WARNING: ASN 7 has a net charge of -0.6880 !!! WARNING: GLN 10 has a net charge of -0.6880 !!! WARNING: ASN 11 has a net charge of -0.6880 !!! WARNING: ARG 12 has a net charge of -0.4460 !!! WARNING: GLN 22 has a net charge of -0.4400 !!! WARNING: ARG 29 has a net charge of -0.4460 !!! WARNING: ASN 36 has a net charge of -0.6880 !!! WARNING: ARG 45 has a net charge of -0.4460 !!! WARNING: ASN 55 has a net charge of -0.6880 !!! WARNING: ASN 69 has a net charge of -0.6880 !!! WARNING: ASN 72 has a net charge of -0.6880 !!! WARNING: ASN 73 has a net charge of -0.6880 !!! WARNING: ARG 78 has a net charge of -0.4460 !!! WARNING: ARG 89 has a net charge of -0.4460 !!! WARNING: ASN 100 has a net charge of -0.6880 !!! WARNING: ASN 113 has a net charge of -0.6880 !!! WARNING: ARG 119 has a net charge of -0.4460 !!! WARNING: ASN 137 has a net charge of -0.6880 !!! WARNING: ARG 153 has a net charge of -0.4460 !!! WARNING: ARG 154 has a net charge of -0.4460 !!! WARNING: GLN 161 has a net charge of -0.6880 !!! WARNING: ASN 164 has a net charge of -0.6880 !!! WARNING: GLN 172 has a net charge of -0.6880 !!! WARNING: GLN 177 has a net charge of -0.6880 !!! WARNING: ARG 185 has a net charge of -0.4460 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 200 has a net charge of -0.6880 !!! WARNING: ARG 209 has a net charge of -0.4460 !!! WARNING: GLN 210 has a net charge of -0.6880 !!! WARNING: ARG 214 has a net charge of -0.4460 !!! WARNING: GLN 224 has a net charge of -0.6880 !!! WARNING: GLY 228 has a net charge of 0.2480 !!! WARNING: THR 238 has a net charge of 0.2480 !!! WARNING: GLN 239 has a net charge of -0.6880 !!! WARNING: ASN 251 has a net charge of -0.9360 !!! WARNING: GLN 253 has a net charge of -0.6880 !!! WARNING: GLN 258 has a net charge of -0.6880 !!! WARNING: ARG 276 has a net charge of -0.4460 !!! WARNING: GLN 279 has a net charge of -0.6880 !!! WARNING: ARG 280 has a net charge of -0.4460 !!! WARNING: GLN 287 has a net charge of -0.6880 !!! WARNING: TRP 292 has a net charge of 0.2480 !!! WARNING: ASP 294 has a net charge of -0.7520 !!! WARNING: GLN 296 has a net charge of -0.6880 !!! WARNING: GLN 299 has a net charge of -0.6880 !!! WARNING: GLN 319 has a net charge of -0.6880 !!! WARNING: ASN 337 has a net charge of -0.6880 !!! WARNING: GLN 338 has a net charge of -0.6880 !!! WARNING: GLN 339 has a net charge of -0.6880 !!! WARNING: GLN 341 has a net charge of -0.6880 !!! WARNING: GLN 343 has a net charge of -0.6880 !!! WARNING: ASN 344 has a net charge of -0.6880 !!! WARNING: ARG 345 has a net charge of -0.4460 !!! WARNING: ASN 351 has a net charge of -0.6880 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ASN 365 has a net charge of -0.6880 !!! WARNING: GLN 369 has a net charge of -0.6880 !!! WARNING: GLN 375 has a net charge of -0.6880 !!! WARNING: ASN 379 has a net charge of -0.6880 !!! WARNING: ASN 380 has a net charge of -0.6880 !!! WARNING: GLN 390 has a net charge of -0.6880 !!! WARNING: ARG 397 has a net charge of -0.4460 !!! WARNING: GLN 398 has a net charge of -0.6880 !!! WARNING: ARG 402 has a net charge of -0.4460 !!! WARNING: ARG 407 has a net charge of -0.4460 !!! WARNING: ASN 408 has a net charge of -0.6880 !!! WARNING: GLN 414 has a net charge of -0.6880 !!! WARNING: GLN 423 has a net charge of -0.6880 !!! WARNING: ARG 425 has a net charge of -0.4460 !!! WARNING: GLN 430 has a net charge of -0.6880 !!! WARNING: ASN 433 has a net charge of -0.6880 !!! WARNING: ARG 436 has a net charge of -0.4460 !!! WARNING: ARG 438 has a net charge of -0.4460 !!! WARNING: ARG 482 has a net charge of -0.4460 !!! WARNING: ASN 506 has a net charge of -0.6880 !!! WARNING: GLN 512 has a net charge of -0.6880 !!! WARNING: ASN 529 has a net charge of -0.6880 !!! WARNING: GLN 534 has a net charge of -0.6880 !!! WARNING: ASN 539 has a net charge of -0.6880 !!! WARNING: ASN 540 has a net charge of -0.6880 !!! WARNING: ASN 550 has a net charge of -0.6880 !!! WARNING: GLN 552 has a net charge of -0.6880 !!! WARNING: ASN 563 has a net charge of -0.4400 !!! WARNING: ARG 564 has a net charge of -0.4460 !!! WARNING: LYS 576 has a net charge of 1.2480 !!! WARNING: ARG 581 has a net charge of -0.4460 !!! WARNING: CYX 589 has a net charge of 0.2480 !!! WARNING: GLU 593 has a net charge of -0.7520 !!! WARNING: LEU 595 has a net charge of 0.2480 !!! WARNING: LYS 599 has a net charge of 1.2480 !!! WARNING: LEU 632 has a net charge of 0.2480 !!! WARNING: LYS 635 has a net charge of 1.2480 !!! WARNING: ARG 641 has a net charge of -0.4460 !!! WARNING: ASN 652 has a net charge of -0.6880 !!! WARNING: TYR 655 has a net charge of 0.2480 !!! WARNING: ASN 665 has a net charge of -0.6880 !!! WARNING: ARG 671 has a net charge of -0.4460 !!! WARNING: ARG 737 has a net charge of -0.1980 !!! WARNING: THR 742 has a net charge of 0.2480 !!! WARNING: GLY 744 has a net charge of 0.2480 !!! WARNING: GLU 757 has a net charge of -0.7520 !!! WARNING: GLN 762 has a net charge of -0.4400 !!! WARNING: ARG 766 has a net charge of -0.1980 !!! WARNING: TRP 844 has a net charge of 0.2480 !!! WARNING: GLU 847 has a net charge of -0.7520 !!! WARNING: GLN 848 has a net charge of -0.6880 !!! WARNING: PHE 850 has a net charge of 0.2480 !!! WARNING: GLN 851 has a net charge of -0.6880 !!! WARNING: LYS 854 has a net charge of 1.2480 !!! WARNING: ILE 858 has a net charge of 0.2480 !!! WARNING: ILE 862 has a net charge of 0.2480 !!! WARNING: PHE 882 has a net charge of 0.2480 !!! WARNING: ASN 889 has a net charge of -0.6880 !!! WARNING: GLN 890 has a net charge of -0.6880 !!! WARNING: GLN 891 has a net charge of -0.6880 !!! WARNING: GLN 893 has a net charge of -0.6880 !!! WARNING: GLN 895 has a net charge of -0.6880 !!! WARNING: ASN 896 has a net charge of -0.6880 !!! WARNING: ARG 897 has a net charge of -0.4460 !!! WARNING: ARG 990 has a net charge of -0.1980 !!! WARNING: LEU 1052 has a net charge of 0.2480 !!! WARNING: ASN 1058 has a net charge of -0.6880 !!! WARNING: GLN 1064 has a net charge of -0.6880 !!! WARNING: PHE 1077 has a net charge of 0.2480 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.953087 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): -2.752000 79.27200 ymin,ymax (A): -14.05600 65.52900 zmin,zma (A): -24.43500 42.42700 x,y,z range (A): 82.02400 79.58500 66.86200 scale (grids/A): 1.953087 object centre (A): 38.26000 25.73650 8.996001 number of atom coordinates read : 6895 total number of charged atoms : 6463 net assigned charge : -82.14730 assigned positive charge : 963.3899 centred at (gu) : 81.67468 92.88296 89.91074 assigned negative charge : -1045.547 centred at (gu) : 81.18633 93.27687 89.56095 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 203149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 76515 mr = 140756 m= 13573 mr = 55474 m= 891 mr = 8539 m= 15 mr = 340 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 1.050000 number of dielectric boundary points 89035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 259 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 51099 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) : 1.302058 object centre at (A) : 38.26000 25.73650 8.996001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4084560 -0.2214871 midg,1,midg; midg,igrid,midg -0.4477609 -0.3078582 1,midg,midg; igrid,midg,midg -1.672800 -0.2497287 gauss-seidel spectral radius is 0.9990029 estimated iterations to convergence 250 setup time was (sec) 1.300000 now iterating at: 13:34:10 rms-change max change #iterations 9.685402 276.8524 at 10iterations 5.296608 125.1731 at 20iterations 2.868432 65.98071 at 30iterations 1.542593 36.78564 at 40iterations 0.8265887 21.86360 at 50iterations 0.4406920 9.567797 at 60iterations 0.2348096 5.243355 at 70iterations 0.1246835 2.904809 at 80iterations 6.6370159E-02 1.448467 at 90iterations 3.5531685E-02 0.8073540 at 100iterations 1.9123355E-02 0.4542961 at 110iterations 1.0508988E-02 0.2459564 at 120iterations 5.9881783E-03 0.1379395 at 130iterations 3.6293664E-03 7.7980042E-02 at 140iterations 2.3610399E-03 5.0323486E-02 at 150iterations 1.6413048E-03 3.3569336E-02 at 160iterations 1.2011199E-03 2.3689270E-02 at 170iterations 9.0605096E-04 1.7410278E-02 at 180iterations finished qdiffx linear iterations at : 13:34:37 total time elapsed so far: 13.84000 # loops : 180 mean,max change (kT/e) : 9.0605096E-04 1.7410278E-02 energy calculations done at 13.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 13:34:38 13.967u 0.223s 0:29.25 48.4% 0+0k 0+0io 0pf+0w