Mon Oct 10 16:21:01 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 Mon Oct 10 2011 at 16:21:01 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5477766 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 0.5477766 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 455.9771 centred at (gu) : 89.74870 88.49835 88.40240 assigned negative charge : -440.9782 centred at (gu) : 89.88184 88.43862 88.39601 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5794 nv = 96 ne = 84 npr = 57247 no. pairs analyzed = 57247 no. exposed pairs = 4101 no. arc points = 30320 no. surface atoms = 1369 nbur = 1613 mkacc time = 9.9999994E-02 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 = 1.568000 m= 240 mr = 2636 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3060 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4070933E-09 7.1615780E-10 midg,1,midg; midg,igrid,midg 8.2324292E-10 9.8762332E-10 1,midg,midg; igrid,midg,midg 2.0415571E-09 5.2997315E-11 gauss-seidel spectral radius is 0.9828277 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 16:21:02 rms-change max change #iterations 7.2872765E-02 12.25175 at 10iterations 4.8821266E-03 0.8836012 at 20iterations 3.3510095E-04 5.1009178E-02 at 30iterations 2.3464230E-05 3.3574104E-03 at 40iterations 1.8800449E-06 2.9230118E-04 at 50iterations finished qdiffx linear iterations at : 16:21:05 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.8800449E-06 2.9230118E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 16:21:05 3.441u 0.159s 0:03.88 92.5% 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 Mon Oct 10 2011 at 16:21:05 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 1.643330 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 1.643330 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 455.9771 centred at (gu) : 89.24542 85.49401 85.20636 assigned negative charge : -440.9782 centred at (gu) : 89.64526 85.31561 85.18785 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18554 mr = 39341 m= 1884 mr = 12146 m= 47 mr = 785 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 796 time to turn everything in is 0.3300000 number of dielectric boundary points 31493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21595 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) : 0.5477766 object centre at (A) : 112.5640 22.59100 57.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7396061E-02 1.2772507E-02 midg,1,midg; midg,igrid,midg 5.9474600E-03 2.4559697E-02 1,midg,midg; igrid,midg,midg 1.5517069E-02 1.2054321E-02 gauss-seidel spectral radius is 0.9982143 estimated iterations to convergence 188 setup time was (sec) 0.5400000 now iterating at: 16:21:06 rms-change max change #iterations 3.388218 158.4550 at 10iterations 1.403292 56.43115 at 20iterations 0.5872445 24.39282 at 30iterations 0.2459778 9.048729 at 40iterations 0.1024334 3.955612 at 50iterations 4.2867657E-02 1.617474 at 60iterations 1.7997148E-02 0.6487026 at 70iterations 7.5498768E-03 0.2888632 at 80iterations 3.1503085E-03 0.1194229 at 90iterations 1.3228998E-03 4.9411774E-02 at 100iterations 5.5467500E-04 2.2701263E-02 at 110iterations 2.3261724E-04 8.3875656E-03 at 120iterations finished qdiffx linear iterations at : 16:21:13 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.3261724E-04 8.3875656E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 16:21:14 7.771u 0.191s 0:08.30 95.9% 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 Mon Oct 10 2011 at 16:21:14 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 2.464995 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 2.464995 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 455.9771 centred at (gu) : 88.86787 83.24085 82.80945 assigned negative charge : -440.9782 centred at (gu) : 89.46785 82.97335 82.78163 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 146381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63230 mr = 96605 m= 18387 mr = 48141 m= 2776 mr = 13394 m= 135 mr = 1616 m= 0 mr = 24 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 2634 time to turn everything in is 0.7800000 number of dielectric boundary points 71129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22545 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) : 1.643330 object centre at (A) : 112.5640 22.59100 57.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2593680 0.1599821 midg,1,midg; midg,igrid,midg 6.8022154E-02 0.3897993 1,midg,midg; igrid,midg,midg 8.9203261E-02 0.4320108 gauss-seidel spectral radius is 0.9991454 estimated iterations to convergence 270 setup time was (sec) 1.020000 now iterating at: 16:21:15 rms-change max change #iterations 8.732860 297.7903 at 10iterations 4.908782 130.2196 at 20iterations 2.746242 70.72681 at 30iterations 1.527240 35.62425 at 40iterations 0.8473662 18.42338 at 50iterations 0.4670834 10.63467 at 60iterations 0.2578894 5.784966 at 70iterations 0.1424380 3.629520 at 80iterations 7.8527845E-02 1.697870 at 90iterations 4.3293010E-02 0.9357493 at 100iterations 2.3779374E-02 0.5066147 at 110iterations 1.3115830E-02 0.3003039 at 120iterations 7.1981219E-03 0.1510010 at 130iterations 3.9628195E-03 8.1750870E-02 at 140iterations 2.1795775E-03 4.5490265E-02 at 150iterations 1.1998763E-03 2.3681641E-02 at 160iterations 6.6000666E-04 1.4610291E-02 at 170iterations 3.6288222E-04 7.9393387E-03 at 180iterations finished qdiffx linear iterations at : 16:21:26 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 3.6288222E-04 7.9393387E-03 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 16:21:26 12.454u 0.190s 0:12.93 97.7% 0+0k 0+0io 0pf+0w