Mon Oct 10 10:21:29 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 10:21:29 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: HIT 237 has a net charge of 0.5140 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: 0.5614699 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 0.5614699 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.014024 assigned positive charge : 423.5238 centred at (gu) : 92.25208 89.85485 89.08990 assigned negative charge : -414.5103 centred at (gu) : 92.50690 89.93335 89.06780 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6172 nv = 96 ne = 84 npr = 55087 no. pairs analyzed = 55087 no. exposed pairs = 4318 no. arc points = 31118 no. surface atoms = 1436 nbur = 1445 mkacc time = 0.1400000 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 = 1.540000 m= 279 mr = 2729 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3132 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0397866E-09 1.0642383E-09 midg,1,midg; midg,igrid,midg 1.9871409E-09 2.1917079E-10 1,midg,midg; igrid,midg,midg 2.1875595E-09 -3.1291911E-09 gauss-seidel spectral radius is 0.9836491 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 10:21:29 rms-change max change #iterations 7.9443090E-02 16.29302 at 10iterations 5.6959223E-03 0.8591557 at 20iterations 4.0179890E-04 6.5460205E-02 at 30iterations 3.0864980E-05 5.2146912E-03 at 40iterations 2.7127801E-06 3.5524368E-04 at 50iterations finished qdiffx linear iterations at : 10:21:32 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.7127801E-06 3.5524368E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 10:21:33 3.595u 0.191s 0:04.13 91.5% 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 10:21:33 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: HIT 237 has a net charge of 0.5140 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: 1.684410 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 1.684410 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.014024 assigned positive charge : 423.5238 centred at (gu) : 96.75567 89.56386 87.26928 assigned negative charge : -414.5103 centred at (gu) : 97.52041 89.79983 87.20314 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 67087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31118 grid for indexing accessible points = 1.400000 m= 19873 mr = 41415 m= 2209 mr = 12417 m= 68 mr = 955 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 340 time to turn everything in is 0.5300000 number of dielectric boundary points 34445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21082 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) : 0.5614699 object centre at (A) : 46.23600 -20.30750 39.68150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8355828E-02 1.4504628E-02 midg,1,midg; midg,igrid,midg 1.0039879E-02 1.1603020E-02 1,midg,midg; igrid,midg,midg 2.6444580E-02 9.4298570E-04 gauss-seidel spectral radius is 0.9983127 estimated iterations to convergence 193 setup time was (sec) 0.8300000 now iterating at: 10:21:34 rms-change max change #iterations 3.443116 183.0070 at 10iterations 1.467202 63.97629 at 20iterations 0.6286481 21.06573 at 30iterations 0.2689062 9.809139 at 40iterations 0.1151216 3.937248 at 50iterations 4.9188770E-02 1.894494 at 60iterations 2.1119351E-02 0.8917427 at 70iterations 9.0741171E-03 0.3344784 at 80iterations 3.8840231E-03 0.1423826 at 90iterations 1.6696831E-03 6.2067032E-02 at 100iterations 7.1806193E-04 2.5360107E-02 at 110iterations 3.0648871E-04 1.0414124E-02 at 120iterations finished qdiffx linear iterations at : 10:21:41 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 3.0648871E-04 1.0414124E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 10:21:41 7.910u 0.223s 0:08.43 96.4% 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 10:21:41 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: HIT 237 has a net charge of 0.5140 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: 2.526614 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 2.526614 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.014024 assigned positive charge : 423.5238 centred at (gu) : 100.1334 89.34560 85.90371 assigned negative charge : -414.5103 centred at (gu) : 101.2804 89.69966 85.80480 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 155441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31118 grid for indexing accessible points = 1.400000 m= 67827 mr = 102433 m= 19590 mr = 50497 m= 3336 mr = 13684 m= 267 mr = 1931 m= 12 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 1054 time to turn everything in is 1.240000 number of dielectric boundary points 77822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21839 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) : 1.684410 object centre at (A) : 46.23600 -20.30750 39.68150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5329720 0.2891287 midg,1,midg; midg,igrid,midg 8.6674422E-02 0.1393118 1,midg,midg; igrid,midg,midg 0.4142755 3.2021057E-02 gauss-seidel spectral radius is 0.9991902 estimated iterations to convergence 277 setup time was (sec) 1.560000 now iterating at: 10:21:43 rms-change max change #iterations 8.897069 307.5641 at 10iterations 5.130093 146.4086 at 20iterations 2.938050 71.39922 at 30iterations 1.672203 43.09588 at 40iterations 0.9455209 24.93153 at 50iterations 0.5339276 12.04550 at 60iterations 0.3013566 6.147570 at 70iterations 0.1693287 3.741654 at 80iterations 9.5110029E-02 2.032411 at 90iterations 5.3288043E-02 1.131882 at 100iterations 2.9907508E-02 0.6155070 at 110iterations 1.6748494E-02 0.3715897 at 120iterations 9.3740337E-03 0.1908198 at 130iterations 5.2434523E-03 0.1074486 at 140iterations 2.9366002E-03 5.8891296E-02 at 150iterations 1.6424329E-03 3.2357216E-02 at 160iterations 9.1839407E-04 1.9275665E-02 at 170iterations 5.1403540E-04 1.1634827E-02 at 180iterations finished qdiffx linear iterations at : 10:21:54 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 5.1403540E-04 1.1634827E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 10:21:55 12.946u 0.333s 0:13.59 97.6% 0+0k 0+0io 0pf+0w