Wed Feb 15 08:55:45 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:45 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 = 2838 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6191520 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 0.6191520 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 89.53410 90.51183 91.83061 assigned negative charge : -415.4865 centred at (gu) : 89.48985 90.43788 92.05403 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7629 nv = 96 ne = 84 npr = 54193 no. pairs analyzed = 54193 no. exposed pairs = 4101 no. arc points = 29919 no. surface atoms = 1355 nbur = 1483 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3640 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2988 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4226202E-08 -1.4830269E-08 midg,1,midg; midg,igrid,midg 9.5427866E-10 1.2588981E-08 1,midg,midg; igrid,midg,midg 3.4233110E-09 8.3408667E-09 gauss-seidel spectral radius is 0.9865328 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 08:55:46 rms-change max change #iterations 0.1288362 20.80980 at 10iterations 1.2042122E-02 1.769421 at 20iterations 1.1629148E-03 0.1855240 at 30iterations 1.3004371E-04 1.6139984E-02 at 40iterations 2.1170894E-05 3.4599304E-03 at 50iterations finished qdiffx linear iterations at : 08:55:49 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.1170894E-05 3.4599304E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 08:55:49 3.294u 0.177s 0:03.79 91.2% 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 Wed Feb 15 2012 at 08:55:49 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 = 2838 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.857456 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 1.857456 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 88.60181 91.53481 95.49151 assigned negative charge : -415.4865 centred at (gu) : 88.46940 91.31342 96.16219 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29919 grid for indexing accessible points = 1.400000 m= 27729 mr = 52761 m= 3902 mr = 18635 m= 177 mr = 2001 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.5700000 number of dielectric boundary points 40158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21129 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) : 0.6191520 object centre at (A) : -1.329500 0.6775007 28.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3832352E-02 -2.1750251E-02 midg,1,midg; midg,igrid,midg -1.4600365E-02 1.9076742E-02 1,midg,midg; igrid,midg,midg 9.3997298E-03 1.9435307E-02 gauss-seidel spectral radius is 0.9986241 estimated iterations to convergence 214 setup time was (sec) 0.8400000 now iterating at: 08:55:50 rms-change max change #iterations 4.227911 164.5078 at 10iterations 1.954466 64.61237 at 20iterations 0.9109854 28.75274 at 30iterations 0.4246643 13.30501 at 40iterations 0.1976523 6.282133 at 50iterations 9.2017002E-02 2.683769 at 60iterations 4.2760547E-02 1.336571 at 70iterations 1.9984344E-02 0.6547852 at 80iterations 9.2809265E-03 0.2898178 at 90iterations 4.3223887E-03 0.1496496 at 100iterations 2.0203961E-03 6.5627813E-02 at 110iterations 9.4548479E-04 2.9419899E-02 at 120iterations finished qdiffx linear iterations at : 08:55:57 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 9.4548479E-04 2.9419899E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 08:55:57 7.664u 0.214s 0:08.20 95.9% 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 Wed Feb 15 2012 at 08:55:57 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 = 2838 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.786184 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 2.786184 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 87.90269 92.30215 98.23722 assigned negative charge : -415.4865 centred at (gu) : 87.70396 91.97009 99.24331 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 189094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29919 grid for indexing accessible points = 1.400000 m= 90590 mr = 129429 m= 30377 mr = 70155 m= 6442 mr = 22364 m= 806 mr = 4281 m= 42 mr = 451 m= 0 mr = 8 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1324 time to turn everything in is 1.400000 number of dielectric boundary points 90663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 21559 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) : 1.857456 object centre at (A) : -1.329500 0.6775007 28.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7862211 -0.1282527 midg,1,midg; midg,igrid,midg -0.1821489 4.4002086E-02 1,midg,midg; igrid,midg,midg 0.1552297 0.2983089 gauss-seidel spectral radius is 0.9992815 estimated iterations to convergence 294 setup time was (sec) 1.670000 now iterating at: 08:55:59 rms-change max change #iterations 10.22745 376.4198 at 10iterations 6.104499 142.1608 at 20iterations 3.603849 80.24950 at 30iterations 2.119991 50.54659 at 40iterations 1.241360 23.88514 at 50iterations 0.7238364 14.48438 at 60iterations 0.4224526 9.036356 at 70iterations 0.2456713 4.874870 at 80iterations 0.1426945 2.708889 at 90iterations 8.2806788E-02 1.545034 at 100iterations 4.7986038E-02 0.8219757 at 110iterations 2.7830983E-02 0.5183487 at 120iterations 1.6102759E-02 0.2883396 at 130iterations 9.3202647E-03 0.1835327 at 140iterations 5.4059732E-03 0.1003151 at 150iterations 3.1306627E-03 6.3282013E-02 at 160iterations 1.8121136E-03 3.2928467E-02 at 170iterations 1.0478760E-03 1.9440651E-02 at 180iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.0478760E-03 1.9440651E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:56:11 12.898u 0.256s 0:13.93 94.3% 0+0k 0+0io 0pf+0w