Mon Oct 10 17:02:03 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 Mon Oct 10 2011 at 17:02:04 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5139310 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): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 0.5139310 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4596 net assigned charge : 5.800023 assigned positive charge : 727.4081 centred at (gu) : 89.85260 90.46704 88.43115 assigned negative charge : -721.6129 centred at (gu) : 89.73066 90.46677 88.40965 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8141 nv = 96 ne = 84 npr = 97418 no. pairs analyzed = 97418 no. exposed pairs = 6239 no. arc points = 43373 no. surface atoms = 2085 nbur = 2758 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 = 1.652000 m= 306 mr = 4183 m= 0 mr = 13 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4173 ## 638 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6321287E-11 1.0802904E-10 midg,1,midg; midg,igrid,midg 8.5481018E-11 1.1029198E-10 1,midg,midg; igrid,midg,midg -2.8727695E-10 4.4082274E-10 gauss-seidel spectral radius is 0.9806451 estimated iterations to convergence 59 setup time was (sec) 0.7400000 now iterating at: 17:02:04 rms-change max change #iterations 7.2081819E-02 11.98854 at 10iterations 4.9866149E-03 0.9086647 at 20iterations 8.5602666E-04 0.1525497 at 30iterations 2.8439000E-04 3.8684845E-02 at 40iterations 1.0888716E-04 1.3088942E-02 at 50iterations finished qdiffx linear iterations at : 17:02:07 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.0888716E-04 1.3088942E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:02:08 3.555u 0.143s 0:04.40 83.8% 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 Mon Oct 10 2011 at 17:02:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.541793 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): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 1.541793 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4596 net assigned charge : 5.800023 assigned positive charge : 727.4081 centred at (gu) : 89.55655 91.39986 85.29179 assigned negative charge : -721.6129 centred at (gu) : 89.19201 91.39990 85.22876 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 92765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43373 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26875 mr = 63609 m= 2240 mr = 17474 m= 46 mr = 870 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 39973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 34636 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) : 0.5139310 object centre at (A) : 10.31550 2.039501 30.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8290983E-03 1.9372370E-02 midg,1,midg; midg,igrid,midg -2.2195992E-03 -1.0044695E-02 1,midg,midg; igrid,midg,midg -1.7926027E-03 1.1954965E-02 gauss-seidel spectral radius is 0.9981518 estimated iterations to convergence 185 setup time was (sec) 0.9900000 now iterating at: 17:02:09 rms-change max change #iterations 3.914129 160.0348 at 10iterations 1.610793 55.23898 at 20iterations 0.6666662 20.64255 at 30iterations 0.2763333 8.536316 at 40iterations 0.1146293 3.729786 at 50iterations 4.7440335E-02 1.443694 at 60iterations 1.9739278E-02 0.6559650 at 70iterations 8.2463184E-03 0.2782211 at 80iterations 3.5022646E-03 0.1119003 at 90iterations 1.5170119E-03 4.9213409E-02 at 100iterations 7.1115390E-04 2.7281761E-02 at 110iterations 3.7398716E-04 1.1631012E-02 at 120iterations finished qdiffx linear iterations at : 17:02:16 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 3.7398716E-04 1.1631012E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 17:02:17 7.776u 0.210s 0:08.84 90.2% 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 Mon Oct 10 2011 at 17:02:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.312689 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): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 2.312689 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4596 net assigned charge : 5.800023 assigned positive charge : 727.4081 centred at (gu) : 89.33455 92.09952 82.93739 assigned negative charge : -721.6129 centred at (gu) : 88.78801 92.09985 82.84312 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 216733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43373 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 96562 mr = 156853 m= 23923 mr = 74924 m= 3134 mr = 16674 m= 183 mr = 1762 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 90251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 36699 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) : 1.541793 object centre at (A) : 10.31550 2.039501 30.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1368223 0.4829106 midg,1,midg; midg,igrid,midg -0.1568919 -0.2642842 1,midg,midg; igrid,midg,midg -2.2446414E-02 0.1666898 gauss-seidel spectral radius is 0.9991788 estimated iterations to convergence 276 setup time was (sec) 1.930000 now iterating at: 17:02:19 rms-change max change #iterations 10.53923 317.0175 at 10iterations 6.089935 138.1680 at 20iterations 3.496263 89.08727 at 30iterations 1.989046 44.40877 at 40iterations 1.128983 22.09707 at 50iterations 0.6393648 14.52556 at 60iterations 0.3600872 6.801830 at 70iterations 0.2028689 4.034363 at 80iterations 0.1140620 2.262684 at 90iterations 6.4061530E-02 1.295905 at 100iterations 3.5856329E-02 0.7538624 at 110iterations 2.0053018E-02 0.3869820 at 120iterations 1.1250084E-02 0.2135582 at 130iterations 6.3073100E-03 0.1263123 at 140iterations 3.5248850E-03 6.9990158E-02 at 150iterations 1.9761333E-03 3.8814545E-02 at 160iterations 1.1072092E-03 1.9541264E-02 at 170iterations 6.2288856E-04 1.2577057E-02 at 180iterations finished qdiffx linear iterations at : 17:02:31 total time elapsed so far: 13.49000 # loops : 180 mean,max change (kT/e) : 6.2288856E-04 1.2577057E-02 energy calculations done at 13.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.67000 DelPhi exited at 17:02:32 13.673u 0.223s 0:14.71 94.4% 0+0k 0+0io 0pf+0w