Sat Oct 15 15:16:47 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 15 2011 at 15:16:47 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 = 3235 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5250040 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 0.5250040 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3081 net assigned charge : 5.500021 assigned positive charge : 498.2231 centred at (gu) : 90.74692 88.28240 86.53488 assigned negative charge : -492.7239 centred at (gu) : 90.83004 88.51820 86.67838 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 63517 no. pairs analyzed = 63517 no. exposed pairs = 4304 no. arc points = 30797 no. surface atoms = 1434 nbur = 1801 mkacc time = 0.1300000 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 = 1.624000 m= 232 mr = 2681 m= 0 mr = 3 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3140 ## 535 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4052353E-09 -1.4315826E-10 midg,1,midg; midg,igrid,midg 1.3235399E-09 -4.2338510E-10 1,midg,midg; igrid,midg,midg 3.1160394E-10 -1.8918137E-10 gauss-seidel spectral radius is 0.9813313 estimated iterations to convergence 60 setup time was (sec) 0.5400000 now iterating at: 15:16:48 rms-change max change #iterations 6.2797502E-02 12.68964 at 10iterations 3.8372865E-03 0.7115993 at 20iterations 2.5077577E-04 4.4242859E-02 at 30iterations 2.0387046E-05 3.7422180E-03 at 40iterations 2.2224715E-06 3.5095215E-04 at 50iterations finished qdiffx linear iterations at : 15:16:51 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.2224715E-06 3.5095215E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 15:16:51 3.405u 0.148s 0:03.96 89.3% 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 15 2011 at 15:16:51 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 = 3235 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.575012 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 1.575012 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3081 net assigned charge : 5.500021 assigned positive charge : 498.2231 centred at (gu) : 92.24014 84.84637 79.60394 assigned negative charge : -492.7239 centred at (gu) : 92.48975 85.55407 80.03481 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17237 mr = 40810 m= 1482 mr = 11031 m= 23 mr = 584 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.4600000 number of dielectric boundary points 29275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23239 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) : 0.5250040 object centre at (A) : 50.39650 5.931999 20.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2017360E-02 -3.7024957E-03 midg,1,midg; midg,igrid,midg 3.2944668E-02 -5.0194017E-03 1,midg,midg; igrid,midg,midg 2.9712629E-03 -1.9896012E-03 gauss-seidel spectral radius is 0.9980561 estimated iterations to convergence 180 setup time was (sec) 0.7400000 now iterating at: 15:16:52 rms-change max change #iterations 3.223399 141.1403 at 10iterations 1.294685 52.51139 at 20iterations 0.5206285 19.93197 at 30iterations 0.2105113 8.015295 at 40iterations 8.5170671E-02 3.553144 at 50iterations 3.4370635E-02 1.210332 at 60iterations 1.3890618E-02 0.5305462 at 70iterations 5.6081493E-03 0.2176456 at 80iterations 2.2738799E-03 8.9379311E-02 at 90iterations 9.1773592E-04 3.4936905E-02 at 100iterations 3.7297953E-04 1.4647484E-02 at 110iterations 1.5106722E-04 5.7907104E-03 at 120iterations finished qdiffx linear iterations at : 15:16:58 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.5106722E-04 5.7907104E-03 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 15:16:59 6.962u 0.158s 0:07.43 95.6% 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 15 2011 at 15:16:59 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 = 3235 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: 2.362518 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 2.362518 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3081 net assigned charge : 5.500021 assigned positive charge : 498.2231 centred at (gu) : 93.36015 82.26947 74.40583 assigned negative charge : -492.7239 centred at (gu) : 93.73456 83.33103 75.05212 start vw surface at 0.1600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 146590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 61901 mr = 100811 m= 15354 mr = 47191 m= 2101 mr = 10798 m= 100 mr = 1167 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 110 time to turn everything in is 1.070000 number of dielectric boundary points 66053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 24599 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) : 1.575012 object centre at (A) : 50.39650 5.931999 20.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3279461 -2.9249566E-02 midg,1,midg; midg,igrid,midg 0.5338761 -7.3809527E-02 1,midg,midg; igrid,midg,midg 1.2345013E-02 -3.4187082E-02 gauss-seidel spectral radius is 0.9990951 estimated iterations to convergence 263 setup time was (sec) 1.360000 now iterating at: 15:17:00 rms-change max change #iterations 8.573936 280.5641 at 10iterations 4.752762 135.6638 at 20iterations 2.620860 81.47421 at 30iterations 1.435495 45.35075 at 40iterations 0.7858482 19.22693 at 50iterations 0.4297789 10.08224 at 60iterations 0.2335131 5.471977 at 70iterations 0.1269716 3.039131 at 80iterations 6.9161505E-02 1.554680 at 90iterations 3.7553031E-02 0.8186579 at 100iterations 2.0367857E-02 0.4650726 at 110iterations 1.1045407E-02 0.2563019 at 120iterations 6.0021528E-03 0.1277657 at 130iterations 3.2517072E-03 8.0611229E-02 at 140iterations 1.7606684E-03 3.6674500E-02 at 150iterations 9.5626520E-04 2.2510529E-02 at 160iterations 5.2106474E-04 1.1356354E-02 at 170iterations 2.8439739E-04 6.3056946E-03 at 180iterations finished qdiffx linear iterations at : 15:17:10 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 2.8439739E-04 6.3056946E-03 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 15:17:10 11.111u 0.162s 0:11.55 97.5% 0+0k 0+0io 0pf+0w