Mon Oct 10 16:57:37 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 16:57:37 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 = 2884 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5179914 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 0.5179914 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2742 net assigned charge : 1.000036 assigned positive charge : 426.6712 centred at (gu) : 90.87267 89.41957 88.52153 assigned negative charge : -425.6724 centred at (gu) : 90.81342 89.36835 88.63628 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5048 nv = 96 ne = 84 npr = 56579 no. pairs analyzed = 56579 no. exposed pairs = 4023 no. arc points = 28536 no. surface atoms = 1339 nbur = 1545 mkacc time = 0.1000000 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 = 1.624000 m= 167 mr = 2358 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7483674E-10 -1.5587362E-10 midg,1,midg; midg,igrid,midg -1.0894820E-10 1.0510055E-10 1,midg,midg; igrid,midg,midg -8.7632852E-11 1.7495903E-10 gauss-seidel spectral radius is 0.9808089 estimated iterations to convergence 60 setup time was (sec) 0.3900000 now iterating at: 16:57:37 rms-change max change #iterations 5.5664919E-02 10.36759 at 10iterations 3.1252471E-03 0.6052761 at 20iterations 2.1144586E-04 4.0277481E-02 at 30iterations 2.2886103E-05 4.4736862E-03 at 40iterations 3.7124721E-06 8.0204010E-04 at 50iterations finished qdiffx linear iterations at : 16:57:40 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 3.7124721E-06 8.0204010E-04 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 16:57:41 3.517u 0.183s 0:04.48 82.3% 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 16:57:41 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 = 2884 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.553974 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 1.553974 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2742 net assigned charge : 1.000036 assigned positive charge : 426.6712 centred at (gu) : 92.61723 88.25789 85.56380 assigned negative charge : -425.6724 centred at (gu) : 92.44000 88.10485 85.90896 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 15805 mr = 35899 m= 1309 mr = 10014 m= 24 mr = 480 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 26696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 379 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 20689 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) : 0.5179914 object centre at (A) : 15.95150 16.88600 31.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3513396E-02 -7.1759345E-03 midg,1,midg; midg,igrid,midg -7.8067952E-03 -1.1355828E-03 1,midg,midg; igrid,midg,midg -1.0830552E-03 1.7632701E-03 gauss-seidel spectral radius is 0.9979844 estimated iterations to convergence 177 setup time was (sec) 0.5300000 now iterating at: 16:57:42 rms-change max change #iterations 2.863357 139.8057 at 10iterations 1.131025 53.60400 at 20iterations 0.4507371 20.81337 at 30iterations 0.1788180 7.254475 at 40iterations 7.1180537E-02 2.769123 at 50iterations 2.8322414E-02 1.094423 at 60iterations 1.1257252E-02 0.4574318 at 70iterations 4.4682021E-03 0.1699219 at 80iterations 1.7786724E-03 6.8927765E-02 at 90iterations 7.0851203E-04 2.8523445E-02 at 100iterations 2.8216906E-04 1.1249542E-02 at 110iterations 1.1308645E-04 4.6691895E-03 at 120iterations finished qdiffx linear iterations at : 16:57:49 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.1308645E-04 4.6691895E-03 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 16:57:50 7.810u 0.204s 0:08.52 94.0% 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 16:57:50 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 = 2884 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.330961 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 2.330961 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2742 net assigned charge : 1.000036 assigned positive charge : 426.6712 centred at (gu) : 93.92571 87.38656 83.34550 assigned negative charge : -425.6724 centred at (gu) : 93.65980 87.15715 83.86333 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 130205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 56361 mr = 88788 m= 14198 mr = 42719 m= 1730 mr = 9841 m= 89 mr = 915 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 60308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21892 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) : 1.553974 object centre at (A) : 15.95150 16.88600 31.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1353763 -0.1014537 midg,1,midg; midg,igrid,midg -0.1008004 -2.5803128E-02 1,midg,midg; igrid,midg,midg -1.0092837E-02 2.2471700E-02 gauss-seidel spectral radius is 0.9990776 estimated iterations to convergence 260 setup time was (sec) 0.9000000 now iterating at: 16:57:51 rms-change max change #iterations 7.797090 248.2641 at 10iterations 4.318303 131.2852 at 20iterations 2.364569 69.62919 at 30iterations 1.290140 30.55782 at 40iterations 0.7018379 20.73745 at 50iterations 0.3781558 9.781940 at 60iterations 0.2050197 4.824226 at 70iterations 0.1102846 2.601830 at 80iterations 5.9371103E-02 1.419720 at 90iterations 3.2042291E-02 0.7273450 at 100iterations 1.7241783E-02 0.3930340 at 110iterations 9.2777712E-03 0.2055655 at 120iterations 4.9787057E-03 0.1081333 at 130iterations 2.6751850E-03 5.8031082E-02 at 140iterations 1.4395769E-03 3.2246590E-02 at 150iterations 7.7446998E-04 1.6920090E-02 at 160iterations 4.1664290E-04 9.1362000E-03 at 170iterations 2.2463969E-04 5.2909851E-03 at 180iterations finished qdiffx linear iterations at : 16:58:02 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 2.2463969E-04 5.2909851E-03 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 16:58:03 12.329u 0.230s 0:13.17 95.2% 0+0k 0+0io 0pf+0w