Tue Nov 22 14:10:13 PST 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 Tue Nov 22 2011 at 14:10:15 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 = 1964 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: 0.6489837 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 0.6489837 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.43030 92.08382 89.94449 assigned negative charge : -284.8263 centred at (gu) : 90.52411 92.20399 89.87912 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5653 nv = 96 ne = 84 npr = 40316 no. pairs analyzed = 40316 no. exposed pairs = 2454 no. arc points = 17212 no. surface atoms = 830 nbur = 1134 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 271 mr = 3133 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2200000 number of dielectric boundary points 2758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1703593E-09 1.2865740E-08 midg,1,midg; midg,igrid,midg 1.2180732E-08 -1.1598013E-08 1,midg,midg; igrid,midg,midg 1.4655422E-08 -4.7387836E-09 gauss-seidel spectral radius is 0.9876403 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 14:10:15 rms-change max change #iterations 0.1298469 22.94558 at 10iterations 1.3327781E-02 2.305854 at 20iterations 1.3409887E-03 0.2271553 at 30iterations 1.3793004E-04 2.3004532E-02 at 40iterations 1.4044798E-05 2.0198822E-03 at 50iterations finished qdiffx linear iterations at : 14:10:20 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.4044798E-05 2.0198822E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 14:10:22 3.176u 0.182s 0:07.82 42.8% 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 Tue Nov 22 2011 at 14:10:27 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 = 1964 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: 1.946951 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 1.946951 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.29096 96.25172 89.83357 assigned negative charge : -284.8263 centred at (gu) : 91.57269 96.61227 89.63770 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 60715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17212 grid for indexing accessible points = 1.400000 m= 22195 mr = 41823 m= 3294 mr = 16964 m= 170 mr = 2103 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1985 time to turn everything in is 0.4300000 number of dielectric boundary points 25430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14462 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) : 0.6489837 object centre at (A) : 14.65750 23.05900 3.777500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5737859E-02 1.3445697E-02 midg,1,midg; midg,igrid,midg 4.6060927E-02 -7.5764148E-03 1,midg,midg; igrid,midg,midg 6.8265726E-03 -4.9269134E-03 gauss-seidel spectral radius is 0.9986152 estimated iterations to convergence 213 setup time was (sec) 0.7100000 now iterating at: 14:10:32 rms-change max change #iterations 3.690395 180.3475 at 10iterations 1.720529 94.84743 at 20iterations 0.8019648 28.20840 at 30iterations 0.3739063 13.44963 at 40iterations 0.1734875 5.772128 at 50iterations 8.0835201E-02 3.144878 at 60iterations 3.7615612E-02 1.370617 at 70iterations 1.7556913E-02 0.6409264 at 80iterations 8.1201820E-03 0.3747698 at 90iterations 3.7914244E-03 0.1318684 at 100iterations 1.7669142E-03 5.6218147E-02 at 110iterations 8.2392053E-04 2.6901245E-02 at 120iterations finished qdiffx linear iterations at : 14:10:48 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 8.2392053E-04 2.6901245E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 14:10:48 7.379u 0.251s 0:22.09 34.4% 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 Tue Nov 22 2011 at 14:10:50 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 = 1964 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: 2.920427 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 2.920427 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.93661 99.37757 89.75038 assigned negative charge : -284.8263 centred at (gu) : 92.35909 99.91853 89.45665 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 139892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17212 grid for indexing accessible points = 1.400000 m= 71638 mr = 100811 m= 26283 mr = 59545 m= 5958 mr = 21799 m= 789 mr = 4565 m= 38 mr = 523 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 6535 time to turn everything in is 1.090000 number of dielectric boundary points 57348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 14655 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) : 1.946951 object centre at (A) : 14.65750 23.05900 3.777500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.036052 1.9048626E-03 midg,1,midg; midg,igrid,midg 0.4867829 -0.1393664 1,midg,midg; igrid,midg,midg 3.6860455E-02 -3.0325359E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.410000 now iterating at: 14:10:58 rms-change max change #iterations 8.613619 367.6482 at 10iterations 4.934251 123.0366 at 20iterations 2.810373 67.74437 at 30iterations 1.601094 36.77558 at 40iterations 0.9137706 19.51543 at 50iterations 0.5195709 9.871660 at 60iterations 0.2949124 6.549412 at 70iterations 0.1676610 3.129494 at 80iterations 9.5427029E-02 1.905073 at 90iterations 5.4393128E-02 1.012974 at 100iterations 3.0960726E-02 0.5962105 at 110iterations 1.7530227E-02 0.3799572 at 120iterations 9.9803936E-03 0.2003651 at 130iterations 5.6731002E-03 0.1113007 at 140iterations 3.2335503E-03 6.2057495E-02 at 150iterations 1.8387402E-03 3.9302826E-02 at 160iterations 1.0430656E-03 2.0481110E-02 at 170iterations 5.9541722E-04 1.2435913E-02 at 180iterations finished qdiffx linear iterations at : 14:11:20 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 5.9541722E-04 1.2435913E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:11:22 11.794u 0.218s 0:31.66 37.9% 0+0k 0+0io 0pf+0w