Sat Oct 15 13:20:59 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 Sat Oct 15 2011 at 13:20:59 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 0.5693814 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): -26.04500 22.68900 ymin,ymax (A): -66.16300 -3.639000 zmin,zma (A): 44.96600 95.10700 x,y,z range (A): 48.73400 62.52400 50.14100 scale (grids/A): 0.5693814 object centre (A): -1.678000 -34.90100 70.03650 number of atom coordinates read : 3088 total number of charged atoms : 2941 net assigned charge : -0.9749913 assigned positive charge : 465.5610 centred at (gu) : 89.74178 90.57175 90.96289 assigned negative charge : -466.5372 centred at (gu) : 89.81873 90.56497 90.84969 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6594 nv = 96 ne = 84 npr = 61822 no. pairs analyzed = 61822 no. exposed pairs = 4035 no. arc points = 28567 no. surface atoms = 1358 nbur = 1730 mkacc time = 0.1100000 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 = 1.512000 m= 277 mr = 3376 m= 1 mr = 17 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 0.2200000 number of dielectric boundary points 3479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6030776E-09 2.0671906E-09 midg,1,midg; midg,igrid,midg -2.4314220E-10 -6.7014311E-11 1,midg,midg; igrid,midg,midg 1.1306706E-09 -1.3362096E-09 gauss-seidel spectral radius is 0.9840966 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 13:20:59 rms-change max change #iterations 9.2881687E-02 15.41988 at 10iterations 6.9497232E-03 1.077799 at 20iterations 5.1546074E-04 7.8689098E-02 at 30iterations 3.9300168E-05 6.3302517E-03 at 40iterations 3.3021608E-06 4.8446655E-04 at 50iterations finished qdiffx linear iterations at : 13:21:03 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 3.3021608E-06 4.8446655E-04 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 13:21:03 3.736u 0.204s 0:04.34 90.5% 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 Sat Oct 15 2011 at 13:21:03 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 1.708144 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): -26.04500 22.68900 ymin,ymax (A): -66.16300 -3.639000 zmin,zma (A): 44.96600 95.10700 x,y,z range (A): 48.73400 62.52400 50.14100 scale (grids/A): 1.708144 object centre (A): -1.678000 -34.90100 70.03650 number of atom coordinates read : 3088 total number of charged atoms : 2941 net assigned charge : -0.9749913 assigned positive charge : 465.5610 centred at (gu) : 89.22437 91.71444 92.88783 assigned negative charge : -466.5372 centred at (gu) : 89.45589 91.69449 92.54892 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28567 grid for indexing accessible points = 1.400000 m= 22925 mr = 48676 m= 2563 mr = 15737 m= 88 mr = 1337 m= 0 mr = 13 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 810 time to turn everything in is 0.3500000 number of dielectric boundary points 32145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22716 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) : 0.5693814 object centre at (A) : -1.678000 -34.90100 70.03650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6790480E-03 7.1001044E-03 midg,1,midg; midg,igrid,midg 3.4770651E-03 4.5611551E-03 1,midg,midg; igrid,midg,midg 6.6203824E-03 -5.1798020E-03 gauss-seidel spectral radius is 0.9983696 estimated iterations to convergence 197 setup time was (sec) 0.5800000 now iterating at: 13:21:04 rms-change max change #iterations 3.787537 153.1084 at 10iterations 1.648495 60.74986 at 20iterations 0.7214014 27.01402 at 30iterations 0.3138864 10.66999 at 40iterations 0.1367399 4.453243 at 50iterations 5.9751552E-02 2.147298 at 60iterations 2.6135677E-02 1.050355 at 70iterations 1.1396002E-02 0.3925726 at 80iterations 4.9835001E-03 0.1709290 at 90iterations 2.1825687E-03 8.2736969E-02 at 100iterations 9.5693959E-04 3.5644531E-02 at 110iterations 4.1950747E-04 1.5111923E-02 at 120iterations finished qdiffx linear iterations at : 13:21:12 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 4.1950747E-04 1.5111923E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 13:21:12 8.375u 0.253s 0:08.93 96.5% 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 Sat Oct 15 2011 at 13:21:12 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 2.562216 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): -26.04500 22.68900 ymin,ymax (A): -66.16300 -3.639000 zmin,zma (A): 44.96600 95.10700 x,y,z range (A): 48.73400 62.52400 50.14100 scale (grids/A): 2.562216 object centre (A): -1.678000 -34.90100 70.03650 number of atom coordinates read : 3088 total number of charged atoms : 2941 net assigned charge : -0.9749913 assigned positive charge : 465.5610 centred at (gu) : 88.83660 92.57147 94.33139 assigned negative charge : -466.5372 centred at (gu) : 89.18376 92.54178 93.82330 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 167681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28567 grid for indexing accessible points = 1.400000 m= 77847 mr = 118795 m= 23479 mr = 61729 m= 4257 mr = 17591 m= 353 mr = 2855 m= 10 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2744 time to turn everything in is 0.9200000 number of dielectric boundary points 72467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 23515 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) : 1.708144 object centre at (A) : -1.678000 -34.90100 70.03650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7674055E-02 0.1172223 midg,1,midg; midg,igrid,midg -0.1385719 0.2248015 1,midg,midg; igrid,midg,midg 8.9593515E-02 -7.2640046E-02 gauss-seidel spectral radius is 0.9992056 estimated iterations to convergence 280 setup time was (sec) 1.180000 now iterating at: 13:21:13 rms-change max change #iterations 9.635367 337.1439 at 10iterations 5.601454 126.2248 at 20iterations 3.215648 73.18463 at 30iterations 1.843136 40.87373 at 40iterations 1.052644 21.14600 at 50iterations 0.5988024 12.53930 at 60iterations 0.3403955 7.014198 at 70iterations 0.1931884 3.792351 at 80iterations 0.1091187 2.159065 at 90iterations 6.1749633E-02 1.199739 at 100iterations 3.4906868E-02 0.6658498 at 110iterations 1.9722324E-02 0.4084404 at 120iterations 1.1126285E-02 0.2218895 at 130iterations 6.2960880E-03 0.1381192 at 140iterations 3.5448920E-03 6.6922188E-02 at 150iterations 2.0044365E-03 3.7179947E-02 at 160iterations 1.1334760E-03 2.1902084E-02 at 170iterations 6.4330437E-04 1.2220383E-02 at 180iterations finished qdiffx linear iterations at : 13:21:26 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 6.4330437E-04 1.2220383E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 13:21:27 13.785u 0.249s 0:15.01 93.4% 0+0k 0+0io 0pf+0w