Sat Oct 8 14:32:48 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+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 Sat Oct 8 2011 at 14:32:48 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 = 3034 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6156507 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 0.6156507 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9999948 assigned positive charge : 454.2685 centred at (gu) : 91.53289 91.68638 91.04913 assigned negative charge : -455.2693 centred at (gu) : 91.57829 91.57182 91.11805 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7476 nv = 96 ne = 84 npr = 64087 no. pairs analyzed = 64087 no. exposed pairs = 3465 no. arc points = 24030 no. surface atoms = 1178 nbur = 1856 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 4320 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.4500000 number of dielectric boundary points 3490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0998208E-09 -6.9304171E-09 midg,1,midg; midg,igrid,midg -5.9368688E-09 1.0275695E-08 1,midg,midg; igrid,midg,midg 1.6575715E-09 -5.4346554E-09 gauss-seidel spectral radius is 0.9863674 estimated iterations to convergence 70 setup time was (sec) 0.7500000 now iterating at: 14:32:50 rms-change max change #iterations 0.1334992 17.88914 at 10iterations 1.2583759E-02 1.622765 at 20iterations 1.1900681E-03 0.1598959 at 30iterations 1.3570639E-04 1.7124176E-02 at 40iterations 1.9409470E-05 2.8381348E-03 at 50iterations finished qdiffx linear iterations at : 14:32:54 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 1.9409470E-05 2.8381348E-03 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 14:32:54 4.885u 0.469s 0:05.61 95.1% 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 Sat Oct 8 2011 at 14:32:54 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 = 3034 !!! WARNING: NAP 500 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.846952 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 1.846952 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9999948 assigned positive charge : 454.2685 centred at (gu) : 94.59788 95.05851 93.14684 assigned negative charge : -455.2693 centred at (gu) : 94.73460 94.71526 93.35392 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 82224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24030 grid for indexing accessible points = 1.400000 m= 28685 mr = 59199 m= 3918 mr = 21319 m= 152 mr = 2346 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 768 time to turn everything in is 0.8500000 number of dielectric boundary points 32082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 22655 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) : 0.6156507 object centre at (A) : 10.86900 16.73250 -13.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5416551E-02 4.5425044E-03 midg,1,midg; midg,igrid,midg -3.1863391E-02 3.9098281E-02 1,midg,midg; igrid,midg,midg 7.8125531E-03 -1.0489186E-02 gauss-seidel spectral radius is 0.9985845 estimated iterations to convergence 211 setup time was (sec) 1.190000 now iterating at: 14:32:56 rms-change max change #iterations 4.422051 209.8114 at 10iterations 2.039539 70.45535 at 20iterations 0.9476908 29.18738 at 30iterations 0.4372330 12.85681 at 40iterations 0.2033420 6.885635 at 50iterations 9.3807846E-02 2.898323 at 60iterations 4.3451153E-02 1.432322 at 70iterations 2.0101858E-02 0.5855637 at 80iterations 9.3057277E-03 0.3004227 at 90iterations 4.3150773E-03 0.1322384 at 100iterations 2.0097017E-03 6.8245888E-02 at 110iterations 9.3268650E-04 2.7518749E-02 at 120iterations finished qdiffx linear iterations at : 14:33:06 total time elapsed so far: 11.35000 # loops : 120 mean,max change (kT/e) : 9.3268650E-04 2.7518749E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 14:33:06 11.569u 0.515s 0:12.37 97.5% 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 14:33:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.770428 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 2.770428 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9999948 assigned positive charge : 454.2685 centred at (gu) : 96.89654 97.58759 94.72006 assigned negative charge : -455.2693 centred at (gu) : 97.10188 97.07285 95.03080 start vw surface at 0.1900000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 190776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24030 grid for indexing accessible points = 1.400000 m= 95461 mr = 143329 m= 32038 mr = 79029 m= 6752 mr = 25649 m= 757 mr = 4975 m= 23 mr = 439 m= 0 mr = 4 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2618 time to turn everything in is 2.180000 number of dielectric boundary points 72382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 23095 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) : 1.846952 object centre at (A) : 10.86900 16.73250 -13.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1689483 0.2161285 midg,1,midg; midg,igrid,midg -0.3055080 0.5285516 1,midg,midg; igrid,midg,midg 0.1041524 -8.4168158E-02 gauss-seidel spectral radius is 0.9992459 estimated iterations to convergence 287 setup time was (sec) 2.550000 now iterating at: 14:33:10 rms-change max change #iterations 10.33418 351.7779 at 10iterations 6.006382 126.2101 at 20iterations 3.459030 68.47498 at 30iterations 1.988743 37.97098 at 40iterations 1.139535 23.89633 at 50iterations 0.6537318 11.40974 at 60iterations 0.3743709 6.847238 at 70iterations 0.2152752 4.183147 at 80iterations 0.1230613 2.432848 at 90iterations 7.0457049E-02 1.308212 at 100iterations 4.0185560E-02 0.6945114 at 110iterations 2.3009220E-02 0.3895950 at 120iterations 1.3140037E-02 0.2243423 at 130iterations 7.5519285E-03 0.1285629 at 140iterations 4.3130433E-03 7.2649002E-02 at 150iterations 2.4759497E-03 4.0908813E-02 at 160iterations 1.4224582E-03 2.4328232E-02 at 170iterations 8.1966654E-04 1.3084412E-02 at 180iterations finished qdiffx linear iterations at : 14:33:27 total time elapsed so far: 19.72000 # loops : 180 mean,max change (kT/e) : 8.1966654E-04 1.3084412E-02 energy calculations done at 19.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.92000 DelPhi exited at 14:33:27 19.927u 0.566s 0:20.77 98.6% 0+0k 0+0io 0pf+0w