Mon Oct 10 17:00:07 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 Mon Oct 10 2011 at 17:00:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5089786 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 0.5089786 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4054 net assigned charge : 5.300038 assigned positive charge : 638.0284 centred at (gu) : 90.21272 91.10487 87.55135 assigned negative charge : -632.7321 centred at (gu) : 90.06990 91.12198 87.57137 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7113 nv = 96 ne = 84 npr = 86791 no. pairs analyzed = 86791 no. exposed pairs = 5630 no. arc points = 38888 no. surface atoms = 1884 nbur = 2413 mkacc time = 0.2000000 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 = 1.652000 m= 261 mr = 3623 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3681 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9393 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1134999E-10 1.4322051E-11 midg,1,midg; midg,igrid,midg 7.8362830E-11 4.1411898E-11 1,midg,midg; igrid,midg,midg -2.2756716E-10 3.8689721E-10 gauss-seidel spectral radius is 0.9802287 estimated iterations to convergence 59 setup time was (sec) 0.6700000 now iterating at: 17:00:08 rms-change max change #iterations 6.1945796E-02 10.50476 at 10iterations 3.5086521E-03 0.5489922 at 20iterations 3.6833517E-04 4.9050331E-02 at 30iterations 1.0999105E-04 1.3133734E-02 at 40iterations 3.9484577E-05 5.4593086E-03 at 50iterations finished qdiffx linear iterations at : 17:00:11 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 3.9484577E-05 5.4593086E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 17:00:11 3.277u 0.163s 0:03.83 89.5% 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 17:00:11 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.526936 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 1.526936 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4054 net assigned charge : 5.300038 assigned positive charge : 638.0284 centred at (gu) : 90.63735 93.31352 82.65240 assigned negative charge : -632.7321 centred at (gu) : 90.20963 93.36588 82.71394 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38888 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22351 mr = 54805 m= 1816 mr = 14277 m= 44 mr = 708 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 30474 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) : 0.5089786 object centre at (A) : 10.19600 -1.138499 30.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9331406E-03 9.6627716E-03 midg,1,midg; midg,igrid,midg -8.6125877E-04 -2.6712227E-03 1,midg,midg; igrid,midg,midg -3.1520552E-03 9.7237471E-03 gauss-seidel spectral radius is 0.9980561 estimated iterations to convergence 180 setup time was (sec) 0.8400000 now iterating at: 17:00:12 rms-change max change #iterations 3.467495 153.9449 at 10iterations 1.399456 53.52478 at 20iterations 0.5624127 20.23123 at 30iterations 0.2286909 7.889795 at 40iterations 9.2371970E-02 3.555138 at 50iterations 3.7463628E-02 1.304192 at 60iterations 1.5187008E-02 0.5135384 at 70iterations 6.1632306E-03 0.2583637 at 80iterations 2.5218856E-03 8.5309029E-02 at 90iterations 1.0462160E-03 3.3806801E-02 at 100iterations 4.4560913E-04 1.7044067E-02 at 110iterations 2.0510016E-04 7.4768066E-03 at 120iterations finished qdiffx linear iterations at : 17:00:19 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 2.0510016E-04 7.4768066E-03 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 17:00:19 7.231u 0.159s 0:07.79 94.7% 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 17:00:19 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.290404 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 2.290404 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4054 net assigned charge : 5.300038 assigned positive charge : 638.0284 centred at (gu) : 90.95554 94.96999 78.97820 assigned negative charge : -632.7321 centred at (gu) : 90.31442 95.04884 79.07083 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 188145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38888 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81136 mr = 134884 m= 19213 mr = 62360 m= 2523 mr = 13379 m= 120 mr = 1438 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 79046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 32338 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) : 1.526936 object centre at (A) : 10.19600 -1.138499 30.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2498464 0.2610829 midg,1,midg; midg,igrid,midg -9.7011596E-02 -0.1236390 1,midg,midg; igrid,midg,midg -4.4911917E-02 0.1305584 gauss-seidel spectral radius is 0.9991360 estimated iterations to convergence 269 setup time was (sec) 1.560000 now iterating at: 17:00:21 rms-change max change #iterations 9.548446 258.2893 at 10iterations 5.414655 144.1473 at 20iterations 3.056231 72.17771 at 30iterations 1.711598 38.19689 at 40iterations 0.9569117 22.18542 at 50iterations 0.5317865 12.01820 at 60iterations 0.2953453 6.275961 at 70iterations 0.1633802 3.592116 at 80iterations 9.0554141E-02 2.202920 at 90iterations 5.0014552E-02 1.100197 at 100iterations 2.7622463E-02 0.5656052 at 110iterations 1.5233468E-02 0.2983818 at 120iterations 8.4180934E-03 0.1659241 at 130iterations 4.6328325E-03 9.7795486E-02 at 140iterations 2.5487482E-03 5.0519943E-02 at 150iterations 1.4018355E-03 2.6622772E-02 at 160iterations 7.7395129E-04 1.5105277E-02 at 170iterations 4.2667269E-04 8.7277293E-03 at 180iterations finished qdiffx linear iterations at : 17:00:30 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 4.2667269E-04 8.7277293E-03 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 17:00:31 11.172u 0.184s 0:11.67 97.2% 0+0k 0+0io 0pf+0w