Mon Oct 10 14:13:13 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 14:13:13 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5229219 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): -2.089000 55.88500 ymin,ymax (A): -18.45100 49.62800 zmin,zma (A): -6.275000 59.08100 x,y,z range (A): 57.97400 68.07899 65.35600 scale (grids/A): 0.5229219 object centre (A): 26.89800 15.58850 26.40300 number of atom coordinates read : 3595 total number of charged atoms : 3446 net assigned charge : -7.999964 assigned positive charge : 540.1238 centred at (gu) : 89.56083 85.57095 90.28865 assigned negative charge : -548.1257 centred at (gu) : 89.62980 85.54566 90.30649 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6372 nv = 96 ne = 84 npr = 71237 no. pairs analyzed = 71237 no. exposed pairs = 4715 no. arc points = 33221 no. surface atoms = 1582 nbur = 2013 mkacc time = 0.1600000 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 = 1.624000 m= 233 mr = 3186 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3390 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1955369E-10 -2.6222946E-10 midg,1,midg; midg,igrid,midg -8.4939505E-10 -3.6830910E-11 1,midg,midg; igrid,midg,midg 4.0763906E-11 -3.6751152E-10 gauss-seidel spectral radius is 0.9812118 estimated iterations to convergence 60 setup time was (sec) 0.5900000 now iterating at: 14:13:14 rms-change max change #iterations 6.5247543E-02 10.38876 at 10iterations 3.8751531E-03 0.5914879 at 20iterations 3.3963114E-04 5.6015015E-02 at 30iterations 6.6123343E-05 1.3251305E-02 at 40iterations 1.7052107E-05 3.4379959E-03 at 50iterations finished qdiffx linear iterations at : 14:13:17 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.7052107E-05 3.4379959E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:13:17 3.384u 0.207s 0:03.93 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 Mon Oct 10 2011 at 14:13:17 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.568766 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): -2.089000 55.88500 ymin,ymax (A): -18.45100 49.62800 zmin,zma (A): -6.275000 59.08100 x,y,z range (A): 57.97400 68.07899 65.35600 scale (grids/A): 1.568766 object centre (A): 26.89800 15.58850 26.40300 number of atom coordinates read : 3595 total number of charged atoms : 3446 net assigned charge : -7.999964 assigned positive charge : 540.1238 centred at (gu) : 88.68159 76.71194 90.86488 assigned negative charge : -548.1257 centred at (gu) : 88.88889 76.63663 90.91908 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33221 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20930 mr = 47554 m= 1827 mr = 13769 m= 52 mr = 720 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 31840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 26065 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) : 0.5229219 object centre at (A) : 26.89800 15.58850 26.40300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9555129E-04 -5.5613136E-03 midg,1,midg; midg,igrid,midg -2.6324259E-02 -2.4530916E-03 1,midg,midg; igrid,midg,midg -5.3872829E-03 -2.3749627E-02 gauss-seidel spectral radius is 0.9980774 estimated iterations to convergence 181 setup time was (sec) 0.8100000 now iterating at: 14:13:18 rms-change max change #iterations 3.390024 158.7975 at 10iterations 1.369560 51.79948 at 20iterations 0.5583091 19.83394 at 30iterations 0.2266999 8.173092 at 40iterations 9.2437319E-02 3.322449 at 50iterations 3.7398078E-02 1.496136 at 60iterations 1.5256180E-02 0.5451965 at 70iterations 6.2434180E-03 0.2627468 at 80iterations 2.5690368E-03 8.7104797E-02 at 90iterations 1.0661221E-03 3.9476395E-02 at 100iterations 4.5841088E-04 1.6069412E-02 at 110iterations 2.0820364E-04 9.0706348E-03 at 120iterations finished qdiffx linear iterations at : 14:13:25 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 2.0820364E-04 9.0706348E-03 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 14:13:25 7.492u 0.214s 0:08.15 94.4% 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 Mon Oct 10 2011 at 14:13:25 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.353149 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): -2.089000 55.88500 ymin,ymax (A): -18.45100 49.62800 zmin,zma (A): -6.275000 59.08100 x,y,z range (A): 57.97400 68.07899 65.35600 scale (grids/A): 2.353149 object centre (A): 26.89800 15.58850 26.40300 number of atom coordinates read : 3595 total number of charged atoms : 3446 net assigned charge : -7.999964 assigned positive charge : 540.1238 centred at (gu) : 88.02207 70.06754 91.29723 assigned negative charge : -548.1257 centred at (gu) : 88.33326 69.95478 91.37864 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 165342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33221 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73965 mr = 116920 m= 19165 mr = 57305 m= 2664 mr = 13628 m= 135 mr = 1547 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 71844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 27507 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) : 1.568766 object centre at (A) : 26.89800 15.58850 26.40300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6869804E-02 8.1454650E-02 midg,1,midg; midg,igrid,midg -0.4561531 -5.8863398E-02 1,midg,midg; igrid,midg,midg -7.6023661E-02 -0.4992363 gauss-seidel spectral radius is 0.9991132 estimated iterations to convergence 265 setup time was (sec) 1.590000 now iterating at: 14:13:27 rms-change max change #iterations 9.057455 344.8126 at 10iterations 5.059583 136.5318 at 20iterations 2.805849 69.03048 at 30iterations 1.551304 35.78989 at 40iterations 0.8549563 19.98450 at 50iterations 0.4694775 9.881512 at 60iterations 0.2573157 5.678416 at 70iterations 0.1412554 3.062359 at 80iterations 7.7092811E-02 1.732529 at 90iterations 4.2186506E-02 0.8103981 at 100iterations 2.3018904E-02 0.4715157 at 110iterations 1.2569390E-02 0.2558336 at 120iterations 6.8694875E-03 0.1495972 at 130iterations 3.7520025E-03 9.0051174E-02 at 140iterations 2.0584287E-03 4.3893814E-02 at 150iterations 1.1330519E-03 2.4037600E-02 at 160iterations 6.2892208E-04 1.3084412E-02 at 170iterations 3.5520692E-04 7.4329376E-03 at 180iterations finished qdiffx linear iterations at : 14:13:38 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 3.5520692E-04 7.4329376E-03 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 14:13:39 12.568u 0.264s 0:13.24 96.8% 0+0k 0+0io 0pf+0w