Sun Oct 9 22:07:33 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 Sun Oct 9 2011 at 22:07:33 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 = 2526 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: 0.6568629 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 0.6568629 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2404 net assigned charge : 7.000012 assigned positive charge : 384.3750 centred at (gu) : 90.77589 89.60703 90.07147 assigned negative charge : -377.3756 centred at (gu) : 90.67892 89.45357 90.05851 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 50523 no. pairs analyzed = 50523 no. exposed pairs = 3091 no. arc points = 22063 no. surface atoms = 1051 nbur = 1475 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3913 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2100000 number of dielectric boundary points 3668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2200 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3832836E-08 1.8903689E-08 midg,1,midg; midg,igrid,midg -1.2425239E-08 3.9735028E-08 1,midg,midg; igrid,midg,midg -7.6295897E-10 3.9222176E-08 gauss-seidel spectral radius is 0.9879826 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 22:07:33 rms-change max change #iterations 0.1559135 22.26855 at 10iterations 1.6291080E-02 2.328752 at 20iterations 1.7223870E-03 0.2467175 at 30iterations 1.8076354E-04 2.6958466E-02 at 40iterations 1.8953466E-05 2.4042130E-03 at 50iterations finished qdiffx linear iterations at : 22:07:36 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.8953466E-05 2.4042130E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 22:07:37 3.453u 0.173s 0:04.10 88.2% 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 Sun Oct 9 2011 at 22:07:37 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 = 2526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.970589 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 1.970589 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2404 net assigned charge : 7.000012 assigned positive charge : 384.3750 centred at (gu) : 92.32727 88.82062 90.21400 assigned negative charge : -377.3756 centred at (gu) : 92.03680 88.36054 90.17542 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22063 grid for indexing accessible points = 1.400000 m= 27227 mr = 53342 m= 4587 mr = 20074 m= 327 mr = 2899 m= 5 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1488 time to turn everything in is 0.3800000 number of dielectric boundary points 33586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18983 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) : 0.6568629 object centre at (A) : 13.20300 4.854501 15.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1331093E-02 -5.7029752E-03 midg,1,midg; midg,igrid,midg 2.4317021E-02 5.1686890E-02 1,midg,midg; igrid,midg,midg -1.5384223E-02 2.0246731E-02 gauss-seidel spectral radius is 0.9987124 estimated iterations to convergence 221 setup time was (sec) 0.6100000 now iterating at: 22:07:38 rms-change max change #iterations 4.411950 170.2826 at 10iterations 2.104705 75.36208 at 20iterations 1.007765 31.82182 at 30iterations 0.4811913 14.45112 at 40iterations 0.2298761 6.871063 at 50iterations 0.1100095 3.260138 at 60iterations 5.2496213E-02 1.784369 at 70iterations 2.5045818E-02 0.7828398 at 80iterations 1.2004985E-02 0.3767490 at 90iterations 5.7545998E-03 0.1955462 at 100iterations 2.7382546E-03 8.7343216E-02 at 110iterations 1.3139655E-03 4.0287256E-02 at 120iterations finished qdiffx linear iterations at : 22:07:45 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.3139655E-03 4.0287256E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 22:07:45 8.008u 0.205s 0:08.51 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 Sun Oct 9 2011 at 22:07:45 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 = 2526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.955883 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 2.955883 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2404 net assigned charge : 7.000012 assigned positive charge : 384.3750 centred at (gu) : 93.49081 88.23086 90.32078 assigned negative charge : -377.3756 centred at (gu) : 93.05517 87.54075 90.26313 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 180240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22063 grid for indexing accessible points = 1.400000 m= 88850 mr = 129664 m= 31757 mr = 72528 m= 8225 mr = 25293 m= 1482 mr = 6307 m= 137 mr = 1106 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 4726 time to turn everything in is 0.9900000 number of dielectric boundary points 75718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19227 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) : 1.970589 object centre at (A) : 13.20300 4.854501 15.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2091967 -0.2638532 midg,1,midg; midg,igrid,midg 0.1138048 0.4565784 1,midg,midg; igrid,midg,midg -0.2607326 0.2421058 gauss-seidel spectral radius is 0.9992800 estimated iterations to convergence 294 setup time was (sec) 1.230000 now iterating at: 22:07:47 rms-change max change #iterations 10.22068 430.1608 at 10iterations 5.952456 120.4700 at 20iterations 3.454812 75.20399 at 30iterations 2.006433 42.16562 at 40iterations 1.162930 21.95811 at 50iterations 0.6748882 13.72180 at 60iterations 0.3904822 6.784657 at 70iterations 0.2261630 4.246986 at 80iterations 0.1310083 2.317095 at 90iterations 7.5708322E-02 1.379254 at 100iterations 4.3750975E-02 0.7460775 at 110iterations 2.5312886E-02 0.4366403 at 120iterations 1.4663997E-02 0.2493882 at 130iterations 8.4706610E-03 0.1710682 at 140iterations 4.8988191E-03 8.4684372E-02 at 150iterations 2.8343634E-03 5.4031372E-02 at 160iterations 1.6393811E-03 2.7754664E-02 at 170iterations 9.4887498E-04 1.7340660E-02 at 180iterations finished qdiffx linear iterations at : 22:07:59 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 9.4887498E-04 1.7340660E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 22:07:59 12.960u 0.223s 0:13.45 97.9% 0+0k 0+0io 0pf+0w