Sat Oct 8 17:03:41 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 8 2011 at 17:03:41 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 = 3524 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5357815 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 0.5357815 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -5.999992 assigned positive charge : 532.8492 centred at (gu) : 89.27666 87.11736 89.55803 assigned negative charge : -538.8508 centred at (gu) : 89.26092 87.11472 89.57357 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 72076 no. pairs analyzed = 72076 no. exposed pairs = 4299 no. arc points = 29491 no. surface atoms = 1451 nbur = 2073 mkacc time = 0.1800000 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= 280 mr = 3455 m= 0 mr = 9 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2991 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7951304E-10 -2.9525157E-10 midg,1,midg; midg,igrid,midg -5.3220345E-10 -1.1578594E-10 1,midg,midg; igrid,midg,midg -3.9535300E-10 -1.3517308E-10 gauss-seidel spectral radius is 0.9820814 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 17:03:42 rms-change max change #iterations 7.4257098E-02 12.46139 at 10iterations 4.7540804E-03 0.6973068 at 20iterations 3.5075541E-04 6.1776161E-02 at 30iterations 5.1508610E-05 9.8648071E-03 at 40iterations 1.1946914E-05 2.3670197E-03 at 50iterations finished qdiffx linear iterations at : 17:03:45 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 1.1946914E-05 2.3670197E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:03:46 4.616u 0.424s 0:05.54 90.7% 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 8 2011 at 17:03:46 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 = 3524 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.607344 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 1.607344 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -5.999992 assigned positive charge : 532.8492 centred at (gu) : 87.82899 81.35161 88.67300 assigned negative charge : -538.8508 centred at (gu) : 87.78236 81.34368 88.72015 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22224 mr = 50111 m= 2161 mr = 15314 m= 52 mr = 960 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 30010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 25759 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) : 0.5357815 object centre at (A) : 30.99650 45.44600 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1435003E-04 -8.4820791E-04 midg,1,midg; midg,igrid,midg -2.1432390E-02 -1.4226032E-02 1,midg,midg; igrid,midg,midg 5.6663365E-03 -3.9061452E-03 gauss-seidel spectral radius is 0.9981613 estimated iterations to convergence 185 setup time was (sec) 0.9000000 now iterating at: 17:03:48 rms-change max change #iterations 3.529524 159.3635 at 10iterations 1.462389 52.19511 at 20iterations 0.6065391 20.46536 at 30iterations 0.2521094 9.993897 at 40iterations 0.1050091 3.729923 at 50iterations 4.3655321E-02 1.410904 at 60iterations 1.8119857E-02 0.6501570 at 70iterations 7.5199930E-03 0.2699299 at 80iterations 3.1381268E-03 0.1053410 at 90iterations 1.3101582E-03 4.9296081E-02 at 100iterations 5.5440114E-04 2.1100998E-02 at 110iterations 2.3775356E-04 8.8519007E-03 at 120iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 10.37000 # loops : 120 mean,max change (kT/e) : 2.3775356E-04 8.8519007E-03 energy calculations done at 10.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 17:03:58 10.540u 0.452s 0:11.30 97.2% 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 8 2011 at 17:03:58 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 = 3524 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.411017 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 2.411017 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -5.999992 assigned positive charge : 532.8492 centred at (gu) : 86.74352 77.02695 88.00945 assigned negative charge : -538.8508 centred at (gu) : 86.67344 77.01550 88.08009 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77684 mr = 122136 m= 21398 mr = 61868 m= 3400 mr = 15923 m= 177 mr = 2182 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 67650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 26985 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) : 1.607344 object centre at (A) : 30.99650 45.44600 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7876845E-02 -1.1991877E-02 midg,1,midg; midg,igrid,midg -0.4154584 -0.2726727 1,midg,midg; igrid,midg,midg 0.3752218 -5.7865642E-02 gauss-seidel spectral radius is 0.9991344 estimated iterations to convergence 269 setup time was (sec) 1.780000 now iterating at: 17:04:00 rms-change max change #iterations 9.222410 293.6671 at 10iterations 5.178763 140.6869 at 20iterations 2.892102 65.76881 at 30iterations 1.609406 34.11261 at 40iterations 0.8907034 19.01081 at 50iterations 0.4922634 11.19781 at 60iterations 0.2717928 5.350138 at 70iterations 0.1498120 3.073219 at 80iterations 8.2493678E-02 1.619579 at 90iterations 4.5380112E-02 0.9044733 at 100iterations 2.4925249E-02 0.5112309 at 110iterations 1.3729978E-02 0.2746267 at 120iterations 7.5404630E-03 0.1683846 at 130iterations 4.1539450E-03 8.3532333E-02 at 140iterations 2.2892256E-03 4.4616699E-02 at 150iterations 1.2661511E-03 2.3926675E-02 at 160iterations 7.0451351E-04 1.4423445E-02 at 170iterations 3.9691350E-04 8.3503723E-03 at 180iterations finished qdiffx linear iterations at : 17:04:15 total time elapsed so far: 17.33000 # loops : 180 mean,max change (kT/e) : 3.9691350E-04 8.3503723E-03 energy calculations done at 17.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.49000 DelPhi exited at 17:04:16 17.493u 0.485s 0:18.23 98.5% 0+0k 0+0io 0pf+0w