Sun Oct 9 13:32:43 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 13:32:43 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 0.6917994 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): -6.044000 44.19500 ymin,ymax (A): -14.32700 37.13300 zmin,zma (A): 2.028000 44.78900 x,y,z range (A): 50.23900 51.46000 42.76100 scale (grids/A): 0.6917994 object centre (A): 19.07550 11.40300 23.40850 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500019 assigned positive charge : 363.5892 centred at (gu) : 89.42135 91.00092 90.71321 assigned negative charge : -360.0895 centred at (gu) : 89.40621 91.17033 90.76666 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7701 nv = 96 ne = 84 npr = 47169 no. pairs analyzed = 47169 no. exposed pairs = 2954 no. arc points = 20821 no. surface atoms = 991 nbur = 1375 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 520 mr = 4352 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2021 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8760 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6868737E-08 -4.0663498E-10 midg,1,midg; midg,igrid,midg 7.1758713E-08 -5.8599063E-08 1,midg,midg; igrid,midg,midg 1.6953695E-08 2.4370232E-08 gauss-seidel spectral radius is 0.9891449 estimated iterations to convergence 78 setup time was (sec) 0.6200000 now iterating at: 13:32:43 rms-change max change #iterations 0.1990906 29.09988 at 10iterations 2.3951435E-02 2.916534 at 20iterations 3.3307734E-03 0.4990044 at 30iterations 6.8542775E-04 0.1179695 at 40iterations 2.0213301E-04 3.3760071E-02 at 50iterations finished qdiffx linear iterations at : 13:32:47 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 2.0213301E-04 3.3760071E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 13:32:47 4.245u 0.243s 0:04.77 93.9% 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 Sun Oct 9 2011 at 13:32:47 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 2.075398 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): -6.044000 44.19500 ymin,ymax (A): -14.32700 37.13300 zmin,zma (A): 2.028000 44.78900 x,y,z range (A): 50.23900 51.46000 42.76100 scale (grids/A): 2.075398 object centre (A): 19.07550 11.40300 23.40850 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500019 assigned positive charge : 363.5892 centred at (gu) : 88.26389 93.00230 92.13936 assigned negative charge : -360.0895 centred at (gu) : 88.21848 93.51070 92.29979 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20821 grid for indexing accessible points = 1.400000 m= 31775 mr = 57248 m= 5754 mr = 23828 m= 562 mr = 3762 m= 10 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 35016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17641 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) : 0.6917994 object centre at (A) : 19.07550 11.40300 23.40850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2789634E-02 1.1634326E-02 midg,1,midg; midg,igrid,midg 1.2880668E-02 -5.6090552E-02 1,midg,midg; igrid,midg,midg 4.4392508E-02 -1.1242514E-02 gauss-seidel spectral radius is 0.9988211 estimated iterations to convergence 231 setup time was (sec) 0.9500000 now iterating at: 13:32:49 rms-change max change #iterations 4.870028 208.6485 at 10iterations 2.388497 80.46046 at 20iterations 1.179148 35.99873 at 30iterations 0.5834312 17.88293 at 40iterations 0.2886863 8.943493 at 50iterations 0.1430926 4.954647 at 60iterations 7.0564345E-02 2.092243 at 70iterations 3.5200931E-02 1.088943 at 80iterations 1.7556949E-02 0.5000706 at 90iterations 8.8186720E-03 0.2526703 at 100iterations 4.4968990E-03 0.1376877 at 110iterations 2.3627479E-03 7.2818756E-02 at 120iterations finished qdiffx linear iterations at : 13:32:57 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 2.3627479E-03 7.2818756E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 13:32:58 9.747u 0.263s 0:10.27 97.3% 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 Sun Oct 9 2011 at 13:32:58 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 3.113097 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): -6.044000 44.19500 ymin,ymax (A): -14.32700 37.13300 zmin,zma (A): 2.028000 44.78900 x,y,z range (A): 50.23900 51.46000 42.76100 scale (grids/A): 3.113097 object centre (A): 19.07550 11.40300 23.40850 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500019 assigned positive charge : 363.5892 centred at (gu) : 87.39581 94.50326 93.20886 assigned negative charge : -360.0895 centred at (gu) : 87.32757 95.26606 93.44965 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 189334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20821 grid for indexing accessible points = 1.400000 m= 100203 mr = 138314 m= 39048 mr = 82663 m= 10737 mr = 32009 m= 2123 mr = 8143 m= 273 mr = 1568 m= 7 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 78869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 17798 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) : 2.075398 object centre at (A) : 19.07550 11.40300 23.40850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4192224 1.0799062E-02 midg,1,midg; midg,igrid,midg 0.2625420 -0.7224360 1,midg,midg; igrid,midg,midg 0.4532084 -0.3907630 gauss-seidel spectral radius is 0.9992949 estimated iterations to convergence 297 setup time was (sec) 2.420000 now iterating at: 13:33:00 rms-change max change #iterations 10.88463 482.0645 at 10iterations 6.459236 133.1643 at 20iterations 3.812986 72.91455 at 30iterations 2.246602 40.86317 at 40iterations 1.326833 24.00981 at 50iterations 0.7801871 14.83049 at 60iterations 0.4565524 8.466034 at 70iterations 0.2683171 4.884050 at 80iterations 0.1571265 2.737828 at 90iterations 9.2277616E-02 1.606873 at 100iterations 5.3951632E-02 0.9178467 at 110iterations 3.1776141E-02 0.5104675 at 120iterations 1.8913385E-02 0.3133087 at 130iterations 1.1360915E-02 0.2030258 at 140iterations 7.0460960E-03 0.1313992 at 150iterations 4.5288503E-03 9.0682983E-02 at 160iterations 3.0813678E-03 7.2502136E-02 at 170iterations 2.2360438E-03 4.8679352E-02 at 180iterations finished qdiffx linear iterations at : 13:33:14 total time elapsed so far: 15.93000 # loops : 180 mean,max change (kT/e) : 2.2360438E-03 4.8679352E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.12000 DelPhi exited at 13:33:14 16.122u 0.256s 0:16.66 98.2% 0+0k 0+0io 0pf+0w