Sat Oct 8 14:41:24 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 14:41:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6514181 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 0.6514181 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9999914 assigned positive charge : 447.5146 centred at (gu) : 89.17338 89.60593 90.99872 assigned negative charge : -448.5154 centred at (gu) : 89.17220 89.49158 90.94656 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8626 nv = 96 ne = 84 npr = 61744 no. pairs analyzed = 61744 no. exposed pairs = 3487 no. arc points = 24262 no. surface atoms = 1179 nbur = 1812 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 5087 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2306 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3803481E-09 9.3030179E-09 midg,1,midg; midg,igrid,midg -2.5200297E-08 1.7118515E-08 1,midg,midg; igrid,midg,midg -2.6287394E-09 -1.5159198E-09 gauss-seidel spectral radius is 0.9878200 estimated iterations to convergence 74 setup time was (sec) 0.6700000 now iterating at: 14:41:25 rms-change max change #iterations 0.1759414 22.50906 at 10iterations 1.8121377E-02 2.298733 at 20iterations 1.9421916E-03 0.2585373 at 30iterations 2.4169011E-04 3.3588409E-02 at 40iterations 4.1416755E-05 6.0958862E-03 at 50iterations finished qdiffx linear iterations at : 14:41:28 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 4.1416755E-05 6.0958862E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 14:41:29 4.256u 0.283s 0:04.85 93.4% 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 Sat Oct 8 2011 at 14:41:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.954254 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 1.954254 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9999914 assigned positive charge : 447.5146 centred at (gu) : 87.51952 88.81736 92.99572 assigned negative charge : -448.5154 centred at (gu) : 87.51631 88.47430 92.83933 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 94053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24262 grid for indexing accessible points = 1.400000 m= 35847 mr = 68374 m= 5920 mr = 27413 m= 372 mr = 3791 m= 2 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.8200000 number of dielectric boundary points 36487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 22455 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) : 0.6514181 object centre at (A) : 15.12200 -1.3500214E-02 21.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3771796E-02 2.0879652E-02 midg,1,midg; midg,igrid,midg -1.1720048E-02 1.8507538E-02 1,midg,midg; igrid,midg,midg -1.3112864E-02 1.0520738E-02 gauss-seidel spectral radius is 0.9987357 estimated iterations to convergence 223 setup time was (sec) 1.140000 now iterating at: 14:41:30 rms-change max change #iterations 4.874884 192.8463 at 10iterations 2.361691 75.33338 at 20iterations 1.136628 31.97380 at 30iterations 0.5512753 15.11508 at 40iterations 0.2654790 7.903667 at 50iterations 0.1277515 3.855013 at 60iterations 6.1893772E-02 1.645020 at 70iterations 2.9926818E-02 0.8324203 at 80iterations 1.4439824E-02 0.4228582 at 90iterations 7.0049944E-03 0.1887960 at 100iterations 3.3850081E-03 0.1068726 at 110iterations 1.6414043E-03 5.4786682E-02 at 120iterations finished qdiffx linear iterations at : 14:41:39 total time elapsed so far: 9.890000 # loops : 120 mean,max change (kT/e) : 1.6414043E-03 5.4786682E-02 energy calculations done at 9.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 14:41:39 10.075u 0.328s 0:10.69 97.1% 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 Sat Oct 8 2011 at 14:41:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.931381 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 2.931381 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9999914 assigned positive charge : 447.5146 centred at (gu) : 86.27913 88.22580 94.49335 assigned negative charge : -448.5154 centred at (gu) : 86.27444 87.71143 94.25895 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 217243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24262 grid for indexing accessible points = 1.400000 m= 115631 mr = 164758 m= 43351 mr = 96795 m= 10893 mr = 35645 m= 1626 mr = 8382 m= 102 mr = 1112 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 2.150000 number of dielectric boundary points 82122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 22760 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) : 1.954254 object centre at (A) : 15.12200 -1.3500214E-02 21.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1044456 0.3317687 midg,1,midg; midg,igrid,midg -7.7907316E-02 0.1961670 1,midg,midg; igrid,midg,midg -2.0293761E-02 0.3263434 gauss-seidel spectral radius is 0.9992886 estimated iterations to convergence 296 setup time was (sec) 2.490000 now iterating at: 14:41:42 rms-change max change #iterations 11.24612 453.2758 at 10iterations 6.632036 153.7180 at 20iterations 3.909524 77.04870 at 30iterations 2.292229 43.34069 at 40iterations 1.344874 23.53333 at 50iterations 0.7866719 13.28085 at 60iterations 0.4582540 7.484940 at 70iterations 0.2672652 4.622986 at 80iterations 0.1562745 2.672013 at 90iterations 9.0763763E-02 1.411579 at 100iterations 5.2907050E-02 0.9088402 at 110iterations 3.0810365E-02 0.4749222 at 120iterations 1.7922120E-02 0.2839575 at 130iterations 1.0431275E-02 0.1865330 at 140iterations 6.0699205E-03 0.1010361 at 150iterations 3.5361301E-03 5.6322098E-02 at 160iterations 2.0526813E-03 3.1890869E-02 at 170iterations 1.1943968E-03 1.9407272E-02 at 180iterations finished qdiffx linear iterations at : 14:41:57 total time elapsed so far: 17.18000 # loops : 180 mean,max change (kT/e) : 1.1943968E-03 1.9407272E-02 energy calculations done at 17.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.37000 DelPhi exited at 14:41:57 17.367u 0.360s 0:18.04 98.2% 0+0k 0+0io 0pf+0w