Mon Oct 10 14:08:36 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 Mon Oct 10 2011 at 14:08:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 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: 0.6156080 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 0.6156080 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 413.6575 centred at (gu) : 89.55025 89.81073 91.64838 assigned negative charge : -405.1582 centred at (gu) : 89.58792 89.80544 91.59647 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6932 nv = 96 ne = 84 npr = 54580 no. pairs analyzed = 54580 no. exposed pairs = 3668 no. arc points = 26279 no. surface atoms = 1228 nbur = 1533 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3558 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2657 ## 303 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8595 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9566555E-09 1.2990597E-08 midg,1,midg; midg,igrid,midg 5.7992771E-09 5.9668706E-09 1,midg,midg; igrid,midg,midg 9.0175787E-09 3.2715533E-09 gauss-seidel spectral radius is 0.9863557 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 14:08:37 rms-change max change #iterations 0.1255746 23.63401 at 10iterations 1.1207867E-02 1.689823 at 20iterations 9.9959143E-04 0.1524010 at 30iterations 1.0150721E-04 1.4721870E-02 at 40iterations 1.5919153E-05 2.7160645E-03 at 50iterations finished qdiffx linear iterations at : 14:08:39 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.5919153E-05 2.7160645E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:08:40 3.379u 0.169s 0:04.16 84.8% 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 Mon Oct 10 2011 at 14:08:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 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: 1.846824 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 1.846824 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 413.6575 centred at (gu) : 88.65037 89.43158 94.94398 assigned negative charge : -405.1582 centred at (gu) : 88.76340 89.41590 94.78900 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76176 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26279 grid for indexing accessible points = 1.400000 m= 25526 mr = 51272 m= 3592 mr = 17756 m= 212 mr = 1976 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3700000 number of dielectric boundary points 34432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20290 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) : 0.6156080 object centre at (A) : 32.01750 33.05900 30.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0968232E-02 3.4189411E-02 midg,1,midg; midg,igrid,midg 1.2316355E-02 2.1762664E-03 1,midg,midg; igrid,midg,midg 1.6662929E-02 2.0002557E-03 gauss-seidel spectral radius is 0.9985684 estimated iterations to convergence 210 setup time was (sec) 0.5800000 now iterating at: 14:08:41 rms-change max change #iterations 4.069153 187.5825 at 10iterations 1.871232 68.98296 at 20iterations 0.8593244 31.80425 at 30iterations 0.3919545 13.09464 at 40iterations 0.1807694 5.756009 at 50iterations 8.3219267E-02 2.613468 at 60iterations 3.8245369E-02 1.152519 at 70iterations 1.7597798E-02 0.5747035 at 80iterations 8.1080142E-03 0.2707243 at 90iterations 3.7366617E-03 0.1312103 at 100iterations 1.7334644E-03 5.6756973E-02 at 110iterations 8.1037125E-04 2.5878906E-02 at 120iterations finished qdiffx linear iterations at : 14:08:48 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 8.1037125E-04 2.5878906E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 14:08:49 7.744u 0.213s 0:08.27 96.1% 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 Mon Oct 10 2011 at 14:08:49 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 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: 2.770236 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 2.770236 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 413.6575 centred at (gu) : 87.97546 89.14723 97.41587 assigned negative charge : -405.1582 centred at (gu) : 88.14495 89.12385 97.18344 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 176347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26279 grid for indexing accessible points = 1.400000 m= 84609 mr = 125031 m= 27781 mr = 67246 m= 6053 mr = 21083 m= 900 mr = 4117 m= 41 mr = 565 m= 0 mr = 2 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 0.9800000 number of dielectric boundary points 77687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20703 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) : 1.846824 object centre at (A) : 32.01750 33.05900 30.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1186756 0.3968537 midg,1,midg; midg,igrid,midg 0.3958946 1.5798051E-02 1,midg,midg; igrid,midg,midg 0.1637035 -6.1135530E-02 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 1.210000 now iterating at: 14:08:50 rms-change max change #iterations 9.844064 298.8909 at 10iterations 5.810755 143.2652 at 20iterations 3.396350 79.96140 at 30iterations 1.975701 44.97421 at 40iterations 1.146455 30.31877 at 50iterations 0.6621437 14.51070 at 60iterations 0.3821605 8.283562 at 70iterations 0.2204607 4.262658 at 80iterations 0.1267516 2.707203 at 90iterations 7.2815388E-02 1.546588 at 100iterations 4.1793048E-02 0.7798805 at 110iterations 2.3954412E-02 0.4367816 at 120iterations 1.3745896E-02 0.2459373 at 130iterations 7.8760162E-03 0.1498947 at 140iterations 4.5240773E-03 8.6628914E-02 at 150iterations 2.5915431E-03 4.8552990E-02 at 160iterations 1.4885626E-03 2.7458191E-02 at 170iterations 8.5362658E-04 1.7552376E-02 at 180iterations finished qdiffx linear iterations at : 14:09:01 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 8.5362658E-04 1.7552376E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 14:09:02 12.625u 0.196s 0:13.49 94.9% 0+0k 0+0io 0pf+0w