Sat Oct 8 16:34:59 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 16:34:59 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: FAD 994 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5425507 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 0.5425507 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4389 net assigned charge : 3.000041 assigned positive charge : 701.3796 centred at (gu) : 91.67975 89.26416 87.32526 assigned negative charge : -698.3831 centred at (gu) : 91.63644 89.18079 87.34342 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8840 nv = 96 ne = 84 npr = 90478 no. pairs analyzed = 90478 no. exposed pairs = 5623 no. arc points = 39268 no. surface atoms = 1894 nbur = 2680 mkacc time = 0.2600000 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 = 1.568000 m= 408 mr = 4761 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.5200000 number of dielectric boundary points 4467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2518052E-10 -2.3029337E-12 midg,1,midg; midg,igrid,midg -7.3416517E-10 7.5042583E-10 1,midg,midg; igrid,midg,midg -1.5470998E-10 8.3254981E-10 gauss-seidel spectral radius is 0.9826107 estimated iterations to convergence 62 setup time was (sec) 0.8000000 now iterating at: 16:35:00 rms-change max change #iterations 8.8994734E-02 15.09476 at 10iterations 6.2787789E-03 0.9060650 at 20iterations 7.0332625E-04 9.7029686E-02 at 30iterations 1.7507280E-04 2.2980690E-02 at 40iterations 5.3686006E-05 7.6441765E-03 at 50iterations finished qdiffx linear iterations at : 16:35:03 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 5.3686006E-05 7.6441765E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 16:35:04 4.270u 0.275s 0:04.84 93.8% 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 Sat Oct 8 2011 at 16:35:04 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: FAD 994 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.627652 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 1.627652 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4389 net assigned charge : 3.000041 assigned positive charge : 701.3796 centred at (gu) : 95.03783 87.79162 81.97472 assigned negative charge : -698.3831 centred at (gu) : 94.90910 87.54213 82.02966 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 99194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39268 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32057 mr = 69327 m= 3653 mr = 22304 m= 111 mr = 1938 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 447 time to turn everything in is 0.8600000 number of dielectric boundary points 41433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 525 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 33609 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) : 0.5425507 object centre at (A) : 48.54250 152.5210 28.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7572474E-03 8.1374543E-03 midg,1,midg; midg,igrid,midg 1.4591762E-02 3.2576282E-02 1,midg,midg; igrid,midg,midg -1.1004561E-02 -1.4380497E-02 gauss-seidel spectral radius is 0.9983326 estimated iterations to convergence 194 setup time was (sec) 1.170000 now iterating at: 16:35:05 rms-change max change #iterations 4.272716 194.4668 at 10iterations 1.842959 70.40375 at 20iterations 0.7929640 34.65789 at 30iterations 0.3438966 10.64709 at 40iterations 0.1484422 4.423859 at 50iterations 6.4514942E-02 2.035048 at 60iterations 2.7943954E-02 0.9077778 at 70iterations 1.2141247E-02 0.3545666 at 80iterations 5.2827923E-03 0.1630764 at 90iterations 2.3205795E-03 6.7687988E-02 at 100iterations 1.0332244E-03 3.1913757E-02 at 110iterations 4.7541221E-04 1.5337467E-02 at 120iterations finished qdiffx linear iterations at : 16:35:13 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 4.7541221E-04 1.5337467E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 16:35:14 9.802u 0.302s 0:10.43 96.8% 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 Sat Oct 8 2011 at 16:35:14 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: FAD 994 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.441478 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 2.441478 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4389 net assigned charge : 3.000041 assigned positive charge : 701.3796 centred at (gu) : 97.55667 86.68707 77.96171 assigned negative charge : -698.3831 centred at (gu) : 97.36353 86.31295 78.04453 start vw surface at 0.2100000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 230509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39268 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 110590 mr = 169218 m= 32926 mr = 88554 m= 5853 mr = 24983 m= 477 mr = 4005 m= 6 mr = 227 m= 0 mr = 2 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 1258 time to turn everything in is 2.160000 number of dielectric boundary points 93372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 35062 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) : 1.627652 object centre at (A) : 48.54250 152.5210 28.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4424617E-02 0.1798162 midg,1,midg; midg,igrid,midg 0.2278695 0.6164584 1,midg,midg; igrid,midg,midg -0.1551028 -0.2513798 gauss-seidel spectral radius is 0.9992134 estimated iterations to convergence 281 setup time was (sec) 2.500000 now iterating at: 16:35:17 rms-change max change #iterations 11.06577 437.9639 at 10iterations 6.405829 173.7693 at 20iterations 3.681943 79.15382 at 30iterations 2.108891 40.45907 at 40iterations 1.206228 22.58372 at 50iterations 0.6872747 12.13457 at 60iterations 0.3897346 7.343781 at 70iterations 0.2213345 4.074664 at 80iterations 0.1252503 2.194944 at 90iterations 7.0962496E-02 1.205036 at 100iterations 4.0185560E-02 0.7330418 at 110iterations 2.2703957E-02 0.3851376 at 120iterations 1.2860590E-02 0.2174587 at 130iterations 7.2676586E-03 0.1339302 at 140iterations 4.1111433E-03 7.3053360E-02 at 150iterations 2.3252757E-03 4.3067932E-02 at 160iterations 1.3149026E-03 2.3144007E-02 at 170iterations 7.4527814E-04 1.2571812E-02 at 180iterations finished qdiffx linear iterations at : 16:35:31 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 7.4527814E-04 1.2571812E-02 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 16:35:32 16.937u 0.313s 0:17.59 98.0% 0+0k 0+0io 0pf+0w