Tue Oct 11 06:28:07 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 Tue Oct 11 2011 at 06:28:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7652293 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 0.7652293 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1356 net assigned charge : 0.5000029 assigned positive charge : 215.3005 centred at (gu) : 91.21850 88.12230 89.17244 assigned negative charge : -214.8003 centred at (gu) : 91.05449 88.01643 89.09433 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6134 nv = 96 ne = 84 npr = 27822 no. pairs analyzed = 27822 no. exposed pairs = 1804 no. arc points = 12869 no. surface atoms = 622 nbur = 817 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 3544 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2200000 number of dielectric boundary points 2962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 973 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6135 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4016698E-08 8.7995510E-08 midg,1,midg; midg,igrid,midg -1.4772034E-07 9.4261885E-08 1,midg,midg; igrid,midg,midg -1.3530860E-07 2.4623210E-07 gauss-seidel spectral radius is 0.9910293 estimated iterations to convergence 86 setup time was (sec) 0.4600000 now iterating at: 06:28:08 rms-change max change #iterations 0.2296181 33.09886 at 10iterations 3.3113867E-02 4.481155 at 20iterations 4.8296722E-03 0.5942430 at 30iterations 7.1598525E-04 9.4201088E-02 at 40iterations 1.2419367E-04 2.0015717E-02 at 50iterations finished qdiffx linear iterations at : 06:28:11 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.2419367E-04 2.0015717E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:28:11 3.298u 0.231s 0:03.90 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 Tue Oct 11 2011 at 06:28:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.295688 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 2.295688 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1356 net assigned charge : 0.5000029 assigned positive charge : 215.3005 centred at (gu) : 93.65609 84.36723 87.51755 assigned negative charge : -214.8003 centred at (gu) : 93.16362 84.04966 87.28331 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12869 grid for indexing accessible points = 1.400000 m= 27804 mr = 44993 m= 6432 mr = 21719 m= 683 mr = 4566 m= 29 mr = 357 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 0.4700000 number of dielectric boundary points 27179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10819 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) : 0.7652293 object centre at (A) : 23.46200 -1.451000 82.50450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8399871E-03 1.7534694E-02 midg,1,midg; midg,igrid,midg -9.9829324E-02 1.5318091E-02 1,midg,midg; igrid,midg,midg 8.3662271E-03 3.3869080E-02 gauss-seidel spectral radius is 0.9989229 estimated iterations to convergence 241 setup time was (sec) 0.7300000 now iterating at: 06:28:12 rms-change max change #iterations 4.306302 179.3404 at 10iterations 2.207531 90.07083 at 20iterations 1.123989 37.18221 at 30iterations 0.5737456 18.20362 at 40iterations 0.2936760 9.735239 at 50iterations 0.1492423 4.689821 at 60iterations 7.6116174E-02 2.628769 at 70iterations 3.8783688E-02 1.332531 at 80iterations 1.9858267E-02 0.6153555 at 90iterations 1.0188396E-02 0.3503709 at 100iterations 5.2105100E-03 0.1693091 at 110iterations 2.6795771E-03 9.1529846E-02 at 120iterations finished qdiffx linear iterations at : 06:28:18 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 2.6795771E-03 9.1529846E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 06:28:19 6.962u 0.188s 0:07.68 92.9% 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 Tue Oct 11 2011 at 06:28:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.443532 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 3.443532 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1356 net assigned charge : 0.5000029 assigned positive charge : 215.3005 centred at (gu) : 95.48420 81.55091 86.27650 assigned negative charge : -214.8003 centred at (gu) : 94.74553 81.07458 85.92500 start vw surface at 0.1400000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 146696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12869 grid for indexing accessible points = 1.400000 m= 83048 mr = 107584 m= 38186 mr = 70149 m= 12487 mr = 32214 m= 2793 mr = 10015 m= 405 mr = 2032 m= 18 mr = 295 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 4834 time to turn everything in is 1.620000 number of dielectric boundary points 61342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 10848 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) : 2.295688 object centre at (A) : 23.46200 -1.451000 82.50450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1752005E-02 0.1235346 midg,1,midg; midg,igrid,midg -1.531926 0.1455405 1,midg,midg; igrid,midg,midg 1.6756721E-02 0.1820778 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 1.930000 now iterating at: 06:28:21 rms-change max change #iterations 9.310506 335.4295 at 10iterations 5.562925 127.4857 at 20iterations 3.309896 72.30090 at 30iterations 1.962282 45.98446 at 40iterations 1.159593 24.71846 at 50iterations 0.6851597 13.47507 at 60iterations 0.4050969 8.098173 at 70iterations 0.2396538 4.992342 at 80iterations 0.1411336 2.687053 at 90iterations 8.3097421E-02 1.571770 at 100iterations 4.9032964E-02 0.9422607 at 110iterations 2.8859187E-02 0.5615463 at 120iterations 1.7087445E-02 0.3163528 at 130iterations 1.0136609E-02 0.1792507 at 140iterations 6.0507250E-03 0.1190338 at 150iterations 3.6701502E-03 7.1432114E-02 at 160iterations 2.3013805E-03 5.2534103E-02 at 170iterations 1.5088302E-03 3.3829689E-02 at 180iterations finished qdiffx linear iterations at : 06:28:32 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.5088302E-03 3.3829689E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 06:28:33 12.659u 0.281s 0:13.69 94.4% 0+0k 0+0io 0pf+0w