Mon Oct 10 19:32:44 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 19:32:44 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 = 2514 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: 0.6067216 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 0.6067216 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.500034 assigned positive charge : 367.4189 centred at (gu) : 89.03614 88.21731 91.92704 assigned negative charge : -358.9199 centred at (gu) : 89.11295 88.20812 91.98679 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6204 nv = 96 ne = 84 npr = 50405 no. pairs analyzed = 50405 no. exposed pairs = 3468 no. arc points = 24218 no. surface atoms = 1171 nbur = 1343 mkacc time = 0.1100000 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 = 1.456000 m= 297 mr = 3033 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2446 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5578985E-09 3.0245453E-09 midg,1,midg; midg,igrid,midg 6.0990129E-09 3.3261536E-09 1,midg,midg; igrid,midg,midg 9.4710684E-09 1.1066001E-09 gauss-seidel spectral radius is 0.9859383 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 19:32:44 rms-change max change #iterations 0.1089483 16.19624 at 10iterations 9.4843395E-03 1.466191 at 20iterations 8.6496799E-04 0.1480293 at 30iterations 9.2574963E-05 1.7050743E-02 at 40iterations 1.3643160E-05 2.9668808E-03 at 50iterations finished qdiffx linear iterations at : 19:32:48 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.3643160E-05 2.9668808E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 19:32:49 4.138u 0.223s 0:04.98 87.3% 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 Mon Oct 10 2011 at 19:32:49 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 = 2514 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.820165 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 1.820165 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.500034 assigned positive charge : 367.4189 centred at (gu) : 87.10812 84.65143 95.78056 assigned negative charge : -358.9199 centred at (gu) : 87.33885 84.62440 95.96024 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24218 grid for indexing accessible points = 1.400000 m= 21822 mr = 42739 m= 3125 mr = 15041 m= 174 mr = 1792 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 18593 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) : 0.6067216 object centre at (A) : 30.22550 9.891001 59.66000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8354533E-02 7.3355534E-03 midg,1,midg; midg,igrid,midg 1.2732488E-02 8.0245230E-03 1,midg,midg; igrid,midg,midg 2.5293758E-02 2.7855465E-02 gauss-seidel spectral radius is 0.9985034 estimated iterations to convergence 205 setup time was (sec) 0.9300000 now iterating at: 19:32:50 rms-change max change #iterations 3.698222 197.7817 at 10iterations 1.658392 56.83547 at 20iterations 0.7512180 28.40133 at 30iterations 0.3374710 13.14579 at 40iterations 0.1527788 5.289917 at 50iterations 6.8525374E-02 2.496644 at 60iterations 3.1031089E-02 1.074442 at 70iterations 1.3997660E-02 0.4452395 at 80iterations 6.3109007E-03 0.2099533 at 90iterations 2.8573165E-03 9.4022751E-02 at 100iterations 1.2938862E-03 4.2770386E-02 at 110iterations 5.9027853E-04 2.3399353E-02 at 120iterations finished qdiffx linear iterations at : 19:32:58 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 5.9027853E-04 2.3399353E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 19:32:59 9.436u 0.271s 0:10.19 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 Mon Oct 10 2011 at 19:32:59 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 = 2514 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.730247 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 2.730247 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.500034 assigned positive charge : 367.4189 centred at (gu) : 85.66208 81.97701 98.67065 assigned negative charge : -358.9199 centred at (gu) : 86.00815 81.93662 98.94042 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 153708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24218 grid for indexing accessible points = 1.400000 m= 70967 mr = 105048 m= 24148 mr = 55330 m= 5313 mr = 18570 m= 707 mr = 3799 m= 47 mr = 445 m= 0 mr = 12 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 71686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19013 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) : 1.820165 object centre at (A) : 30.22550 9.891001 59.66000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4693992 -3.7161198E-02 midg,1,midg; midg,igrid,midg 0.1717463 9.2551947E-02 1,midg,midg; igrid,midg,midg 0.2148175 0.5273121 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 19:33:01 rms-change max change #iterations 9.001585 298.9626 at 10iterations 5.233014 117.6020 at 20iterations 3.026921 76.56534 at 30iterations 1.739136 37.12249 at 40iterations 0.9980423 20.30801 at 50iterations 0.5698760 11.73944 at 60iterations 0.3255548 7.032338 at 70iterations 0.1854933 3.879896 at 80iterations 0.1054557 2.024341 at 90iterations 5.9953563E-02 1.224839 at 100iterations 3.4067385E-02 0.7334061 at 110iterations 1.9343575E-02 0.4045348 at 120iterations 1.0986840E-02 0.2260208 at 130iterations 6.2568258E-03 0.1253386 at 140iterations 3.5517842E-03 7.1289063E-02 at 150iterations 2.0231626E-03 4.1634083E-02 at 160iterations 1.1504665E-03 2.2325277E-02 at 170iterations 6.5580802E-04 1.3444901E-02 at 180iterations finished qdiffx linear iterations at : 19:33:14 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 6.5580802E-04 1.3444901E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.07000 DelPhi exited at 19:33:15 15.076u 0.278s 0:15.70 97.7% 0+0k 0+0io 0pf+0w