Sun Oct 9 10:56:58 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 Sun Oct 9 2011 at 10:56:58 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 = 2585 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: 0.6132116 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 0.6132116 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.499991 assigned positive charge : 371.6106 centred at (gu) : 90.00726 88.42227 91.28426 assigned negative charge : -375.1118 centred at (gu) : 90.09782 88.50158 91.48317 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6750 nv = 96 ne = 84 npr = 51392 no. pairs analyzed = 51392 no. exposed pairs = 3496 no. arc points = 25154 no. surface atoms = 1183 nbur = 1402 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 349 mr = 3452 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3300000 number of dielectric boundary points 3611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8108 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9746590E-09 -1.7183782E-08 midg,1,midg; midg,igrid,midg 2.8379350E-09 -4.5018869E-09 1,midg,midg; igrid,midg,midg 2.5088454E-09 -6.9870669E-09 gauss-seidel spectral radius is 0.9862443 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 10:56:58 rms-change max change #iterations 0.1173033 19.43133 at 10iterations 1.0289095E-02 1.775120 at 20iterations 9.1801485E-04 0.1512299 at 30iterations 8.5514315E-05 1.4987946E-02 at 40iterations 1.1036322E-05 1.9459724E-03 at 50iterations finished qdiffx linear iterations at : 10:57:01 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1036322E-05 1.9459724E-03 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 10:57:02 3.400u 0.213s 0:04.04 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 Sun Oct 9 2011 at 10:57:02 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 = 2585 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: 1.839635 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 1.839635 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.499991 assigned positive charge : 371.6106 centred at (gu) : 90.02100 85.26658 93.85195 assigned negative charge : -375.1118 centred at (gu) : 90.29336 85.50445 94.44945 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 24632 mr = 48730 m= 3849 mr = 17159 m= 211 mr = 2237 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 33480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19137 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) : 0.6132116 object centre at (A) : 8.387499 44.73350 59.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9304208E-02 -4.0114596E-02 midg,1,midg; midg,igrid,midg 1.3854695E-02 -8.8757817E-03 1,midg,midg; igrid,midg,midg -1.9723503E-02 -2.6027117E-02 gauss-seidel spectral radius is 0.9985610 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 10:57:03 rms-change max change #iterations 3.901067 171.8432 at 10iterations 1.778161 68.94238 at 20iterations 0.8140461 26.81167 at 30iterations 0.3719933 11.91547 at 40iterations 0.1702527 5.651252 at 50iterations 7.8239538E-02 2.917920 at 60iterations 3.5854876E-02 1.127972 at 70iterations 1.6425313E-02 0.5281563 at 80iterations 7.5386707E-03 0.2530594 at 90iterations 3.4556179E-03 0.1157265 at 100iterations 1.5871925E-03 5.1622391E-02 at 110iterations 7.2819745E-04 2.3082733E-02 at 120iterations finished qdiffx linear iterations at : 10:57:09 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 7.2819745E-04 2.3082733E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 10:57:09 7.032u 0.170s 0:07.62 94.4% 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 Sun Oct 9 2011 at 10:57:09 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 = 2585 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: 2.759452 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): -20.64000 37.41500 ymin,ymax (A): 18.79700 70.67000 zmin,zma (A): 30.79400 88.35201 x,y,z range (A): 58.05500 51.87300 57.55801 scale (grids/A): 2.759452 object centre (A): 8.387499 44.73350 59.57300 number of atom coordinates read : 2585 total number of charged atoms : 2443 net assigned charge : -3.499991 assigned positive charge : 371.6106 centred at (gu) : 90.03130 82.89958 95.77768 assigned negative charge : -375.1118 centred at (gu) : 90.44002 83.25669 96.67426 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 169061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 80043 mr = 118939 m= 28108 mr = 63260 m= 6830 mr = 21841 m= 895 mr = 4856 m= 32 mr = 509 m= 0 mr = 4 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 75560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19541 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) : 1.839635 object centre at (A) : 8.387499 44.73350 59.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2300144 -0.1214803 midg,1,midg; midg,igrid,midg 0.2110543 -0.1482658 1,midg,midg; igrid,midg,midg -0.3327024 -0.2526094 gauss-seidel spectral radius is 0.9992470 estimated iterations to convergence 288 setup time was (sec) 1.530000 now iterating at: 10:57:11 rms-change max change #iterations 9.457356 268.7512 at 10iterations 5.567308 149.3615 at 20iterations 3.242653 70.48676 at 30iterations 1.884905 37.55539 at 40iterations 1.086986 22.45777 at 50iterations 0.6279501 12.27145 at 60iterations 0.3607769 7.474371 at 70iterations 0.2071249 4.020376 at 80iterations 0.1188768 2.324367 at 90iterations 6.8243280E-02 1.334248 at 100iterations 3.9007917E-02 0.7159028 at 110iterations 2.2393798E-02 0.4647503 at 120iterations 1.2802555E-02 0.2543945 at 130iterations 7.3128021E-03 0.1369457 at 140iterations 4.1836244E-03 7.5183868E-02 at 150iterations 2.3999943E-03 4.4514656E-02 at 160iterations 1.3712298E-03 2.4050713E-02 at 170iterations 7.8697404E-04 1.3740540E-02 at 180iterations finished qdiffx linear iterations at : 10:57:20 total time elapsed so far: 10.83000 # loops : 180 mean,max change (kT/e) : 7.8697404E-04 1.3740540E-02 energy calculations done at 10.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 10:57:21 11.008u 0.178s 0:11.78 94.8% 0+0k 0+0io 0pf+0w