Sat Oct 15 15:30:45 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 Sat Oct 15 2011 at 15:30:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 0.7109336 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 0.7109336 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.24002 90.10581 90.22089 assigned negative charge : -318.8441 centred at (gu) : 89.36185 90.05119 90.30311 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7269 nv = 96 ne = 84 npr = 42535 no. pairs analyzed = 42535 no. exposed pairs = 2588 no. arc points = 17459 no. surface atoms = 885 nbur = 1442 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4216 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1638 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9334997E-08 1.4293768E-08 midg,1,midg; midg,igrid,midg 2.8575874E-08 9.0583811E-08 1,midg,midg; igrid,midg,midg 1.4467601E-07 -6.6245183E-09 gauss-seidel spectral radius is 0.9896895 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 15:30:46 rms-change max change #iterations 0.2056325 25.33186 at 10iterations 2.5728256E-02 3.504753 at 20iterations 3.4351514E-03 0.4595804 at 30iterations 5.4671225E-04 8.3850861E-02 at 40iterations 1.2556235E-04 1.5052795E-02 at 50iterations finished qdiffx linear iterations at : 15:30:49 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.2556235E-04 1.5052795E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 15:30:49 3.476u 0.193s 0:04.02 91.0% 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 15:30:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 2.132801 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 2.132801 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.72004 90.31734 90.66251 assigned negative charge : -318.8441 centred at (gu) : 88.08579 90.15359 90.90944 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17459 grid for indexing accessible points = 1.400000 m= 31799 mr = 55063 m= 6481 mr = 24454 m= 612 mr = 4426 m= 19 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15902 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) : 0.7109336 object centre at (A) : 49.17550 6.550501 25.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1646241E-02 3.1622481E-02 midg,1,midg; midg,igrid,midg 4.9753211E-02 2.8944533E-02 1,midg,midg; igrid,midg,midg 4.3911152E-02 -5.0443780E-02 gauss-seidel spectral radius is 0.9988456 estimated iterations to convergence 233 setup time was (sec) 0.6300000 now iterating at: 15:30:50 rms-change max change #iterations 4.695200 205.7757 at 10iterations 2.338719 74.59197 at 20iterations 1.159517 34.29853 at 30iterations 0.5788323 18.79637 at 40iterations 0.2886054 9.232243 at 50iterations 0.1440929 4.537279 at 60iterations 7.1905009E-02 2.517711 at 70iterations 3.5942238E-02 0.9675827 at 80iterations 1.7971775E-02 0.5232337 at 90iterations 9.0090381E-03 0.2559967 at 100iterations 4.5579253E-03 0.1343031 at 110iterations 2.3540889E-03 7.0110321E-02 at 120iterations finished qdiffx linear iterations at : 15:30:59 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 2.3540889E-03 7.0110321E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 15:30:59 8.190u 0.241s 0:10.20 82.6% 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 15:30:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 3.199201 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 3.199201 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.57983 90.47598 90.99367 assigned negative charge : -318.8441 centred at (gu) : 87.12867 90.23041 91.36421 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 178073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17459 grid for indexing accessible points = 1.400000 m= 98145 mr = 132469 m= 40960 mr = 82161 m= 12311 mr = 33939 m= 2582 mr = 9760 m= 320 mr = 1911 m= 13 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16016 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) : 2.132801 object centre at (A) : 49.17550 6.550501 25.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1166311 0.2500739 midg,1,midg; midg,igrid,midg 0.4230540 0.1524210 1,midg,midg; igrid,midg,midg 0.4125723 -0.6250257 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 1.460000 now iterating at: 15:31:01 rms-change max change #iterations 10.44248 386.2093 at 10iterations 6.184931 138.7557 at 20iterations 3.663994 72.27205 at 30iterations 2.163917 42.75375 at 40iterations 1.273883 24.83313 at 50iterations 0.7492427 13.58139 at 60iterations 0.4403889 7.682334 at 70iterations 0.2588706 4.562511 at 80iterations 0.1516908 2.759605 at 90iterations 8.9166209E-02 1.552382 at 100iterations 5.2168641E-02 0.8991406 at 110iterations 3.0778501E-02 0.5243332 at 120iterations 1.8163329E-02 0.3119154 at 130iterations 1.0848826E-02 0.2049561 at 140iterations 6.5617529E-03 0.1138802 at 150iterations 4.0896707E-03 7.3295593E-02 at 160iterations 2.6561054E-03 5.4260254E-02 at 170iterations 1.8294235E-03 3.3607483E-02 at 180iterations finished qdiffx linear iterations at : 15:31:14 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.8294235E-03 3.3607483E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 15:31:14 13.223u 0.223s 0:14.81 90.7% 0+0k 0+0io 0pf+0w