Mon Oct 10 19:38:11 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 19:38:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6420546 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 0.6420546 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.499983 assigned positive charge : 288.9033 centred at (gu) : 89.67542 88.14749 87.75142 assigned negative charge : -294.4031 centred at (gu) : 89.54182 88.25025 88.00840 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5727 nv = 96 ne = 84 npr = 42030 no. pairs analyzed = 42030 no. exposed pairs = 2837 no. arc points = 20471 no. surface atoms = 952 nbur = 1095 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 2791 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1600000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1914 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6691 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3468957E-08 -2.0890964E-08 midg,1,midg; midg,igrid,midg 7.4789408E-10 -1.2716176E-08 1,midg,midg; igrid,midg,midg -2.3256080E-08 2.8612082E-09 gauss-seidel spectral radius is 0.9873931 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 19:38:12 rms-change max change #iterations 0.1313214 24.59912 at 10iterations 1.2995819E-02 1.992790 at 20iterations 1.2789347E-03 0.1744738 at 30iterations 1.2395019E-04 2.1553040E-02 at 40iterations 1.2587837E-05 1.7623901E-03 at 50iterations finished qdiffx linear iterations at : 19:38:15 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.2587837E-05 1.7623901E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 19:38:15 3.313u 0.152s 0:03.78 91.5% 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 19:38:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926164 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 1.926164 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.499983 assigned positive charge : 288.9033 centred at (gu) : 89.02644 84.44274 83.25455 assigned negative charge : -294.4031 centred at (gu) : 88.62555 84.75082 84.02523 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 61413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20471 grid for indexing accessible points = 1.400000 m= 19522 mr = 39219 m= 2658 mr = 13349 m= 122 mr = 1514 m= 0 mr = 50 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 973 time to turn everything in is 0.2900000 number of dielectric boundary points 29583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 15100 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) : 0.6420546 object centre at (A) : -7.5999260E-02 5.480499 5.671000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6989729E-02 -3.7351269E-02 midg,1,midg; midg,igrid,midg -4.1272435E-03 -1.1850598E-02 1,midg,midg; igrid,midg,midg -1.4845571E-02 -1.7733988E-03 gauss-seidel spectral radius is 0.9986189 estimated iterations to convergence 213 setup time was (sec) 0.5000000 now iterating at: 19:38:16 rms-change max change #iterations 3.703286 152.0083 at 10iterations 1.731671 68.61594 at 20iterations 0.8024794 29.71444 at 30iterations 0.3728628 12.99014 at 40iterations 0.1735312 5.865445 at 50iterations 8.0824263E-02 2.969635 at 60iterations 3.7538812E-02 1.296096 at 70iterations 1.7453589E-02 0.6383293 at 80iterations 8.1336061E-03 0.3145981 at 90iterations 3.7797454E-03 0.1405439 at 100iterations 1.7673444E-03 6.3988686E-02 at 110iterations 8.2071347E-04 2.9443741E-02 at 120iterations finished qdiffx linear iterations at : 19:38:23 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 8.2071347E-04 2.9443741E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 19:38:23 7.574u 0.198s 0:08.05 96.3% 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 19:38:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.889246 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 2.889246 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.499983 assigned positive charge : 288.9033 centred at (gu) : 88.53957 81.66418 79.88177 assigned negative charge : -294.4031 centred at (gu) : 87.93847 82.12624 81.03789 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20471 grid for indexing accessible points = 1.400000 m= 64548 mr = 96040 m= 21273 mr = 50224 m= 4445 mr = 16185 m= 556 mr = 3188 m= 22 mr = 392 m= 0 mr = 11 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3219 time to turn everything in is 0.7600000 number of dielectric boundary points 66596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15331 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) : 1.926164 object centre at (A) : -7.5999260E-02 5.480499 5.671000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8890774 -0.3431398 midg,1,midg; midg,igrid,midg -0.5039216 -0.1663011 1,midg,midg; igrid,midg,midg -0.1302201 -4.7605619E-02 gauss-seidel spectral radius is 0.9992632 estimated iterations to convergence 291 setup time was (sec) 1.000000 now iterating at: 19:38:25 rms-change max change #iterations 8.794392 380.2782 at 10iterations 5.137245 142.6109 at 20iterations 2.987906 68.35995 at 30iterations 1.724516 37.15739 at 40iterations 0.9974172 22.14805 at 50iterations 0.5760355 11.59719 at 60iterations 0.3314397 7.245110 at 70iterations 0.1915867 4.586220 at 80iterations 0.1099107 2.260187 at 90iterations 6.3228488E-02 1.218246 at 100iterations 3.6322102E-02 0.8942499 at 110iterations 2.0838600E-02 0.4418335 at 120iterations 1.1975549E-02 0.2822008 at 130iterations 6.8811397E-03 0.1387289 at 140iterations 3.9573950E-03 8.4064484E-02 at 150iterations 2.2720799E-03 4.6539307E-02 at 160iterations 1.3014877E-03 2.8203011E-02 at 170iterations 7.4727321E-04 1.4781952E-02 at 180iterations finished qdiffx linear iterations at : 19:38:36 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.4727321E-04 1.4781952E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 19:38:36 12.279u 0.189s 0:12.77 97.4% 0+0k 0+0io 0pf+0w