Mon Oct 10 17:10:53 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 Mon Oct 10 2011 at 17:10:53 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 = 2980 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: 0.5410334 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 0.5410334 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.499973 assigned positive charge : 446.0130 centred at (gu) : 90.62865 90.27885 89.81995 assigned negative charge : -449.5141 centred at (gu) : 90.71428 90.16263 89.73528 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5625 nv = 96 ne = 84 npr = 59792 no. pairs analyzed = 59792 no. exposed pairs = 3900 no. arc points = 27487 no. surface atoms = 1302 nbur = 1678 mkacc time = 0.2100000 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 = 1.596000 m= 222 mr = 2796 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4300000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2732 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7391 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8367495E-10 2.7761937E-10 midg,1,midg; midg,igrid,midg -7.7755069E-10 4.9707999E-10 1,midg,midg; igrid,midg,midg 2.5151048E-10 -7.7189960E-10 gauss-seidel spectral radius is 0.9823933 estimated iterations to convergence 62 setup time was (sec) 0.7600000 now iterating at: 17:10:54 rms-change max change #iterations 6.8617016E-02 10.93703 at 10iterations 4.4394569E-03 0.7422128 at 20iterations 2.8381968E-04 4.6262741E-02 at 30iterations 1.9000870E-05 3.2005310E-03 at 40iterations 1.2951307E-06 2.2935867E-04 at 50iterations finished qdiffx linear iterations at : 17:10:58 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.2951307E-06 2.2935867E-04 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 17:10:59 4.530u 0.419s 0:05.33 92.6% 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 17:10:59 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 = 2980 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: 1.623100 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 1.623100 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.499973 assigned positive charge : 446.0130 centred at (gu) : 91.88508 90.83560 89.45926 assigned negative charge : -449.5141 centred at (gu) : 92.14246 90.48778 89.20567 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18628 mr = 41034 m= 1865 mr = 12525 m= 53 mr = 827 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.6200000 number of dielectric boundary points 28318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21706 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) : 0.5410334 object centre at (A) : 1.976002 1.092000 15.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8068416E-03 4.0436885E-03 midg,1,midg; midg,igrid,midg -1.4665429E-02 6.0968013E-03 1,midg,midg; igrid,midg,midg -1.0515196E-03 -2.1460710E-02 gauss-seidel spectral radius is 0.9981619 estimated iterations to convergence 185 setup time was (sec) 0.9300000 now iterating at: 17:11:00 rms-change max change #iterations 3.262001 155.5992 at 10iterations 1.338427 56.47991 at 20iterations 0.5544760 20.51156 at 30iterations 0.2295088 8.001709 at 40iterations 9.4954878E-02 3.274366 at 50iterations 3.9275512E-02 1.494301 at 60iterations 1.6321519E-02 0.6076088 at 70iterations 6.7732185E-03 0.2978067 at 80iterations 2.7981414E-03 0.1019878 at 90iterations 1.1663989E-03 4.3807983E-02 at 100iterations 4.8151237E-04 1.7729282E-02 at 110iterations 2.0128598E-04 6.8702698E-03 at 120iterations finished qdiffx linear iterations at : 17:11:09 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 2.0128598E-04 6.8702698E-03 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 17:11:09 9.862u 0.476s 0:10.66 96.9% 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 17:11:09 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 = 2980 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: 2.434650 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 2.434650 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.499973 assigned positive charge : 446.0130 centred at (gu) : 92.82747 91.25317 89.18856 assigned negative charge : -449.5141 centred at (gu) : 93.21345 90.73151 88.80835 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 144166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64916 mr = 100697 m= 18032 mr = 50484 m= 2759 mr = 13269 m= 172 mr = 1652 m= 0 mr = 78 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 1815 time to turn everything in is 1.570000 number of dielectric boundary points 63865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 22685 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) : 1.623100 object centre at (A) : 1.976002 1.092000 15.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3779891E-02 6.3117981E-02 midg,1,midg; midg,igrid,midg -0.2105255 0.1174801 1,midg,midg; igrid,midg,midg 0.2279495 -0.5181177 gauss-seidel spectral radius is 0.9991347 estimated iterations to convergence 269 setup time was (sec) 1.940000 now iterating at: 17:11:12 rms-change max change #iterations 8.596389 357.9097 at 10iterations 4.820755 134.9593 at 20iterations 2.675386 60.64251 at 30iterations 1.486298 40.56555 at 40iterations 0.8233747 17.38210 at 50iterations 0.4531939 9.584208 at 60iterations 0.2496279 5.379158 at 70iterations 0.1376522 3.292793 at 80iterations 7.5644039E-02 1.554567 at 90iterations 4.1491583E-02 0.8995438 at 100iterations 2.2748083E-02 0.4977245 at 110iterations 1.2495964E-02 0.2714539 at 120iterations 6.8513039E-03 0.1365356 at 130iterations 3.7623218E-03 7.8397751E-02 at 140iterations 2.0594841E-03 4.6663165E-02 at 150iterations 1.1343602E-03 2.6428223E-02 at 160iterations 6.1980047E-04 1.3729572E-02 at 170iterations 3.3997002E-04 7.0419312E-03 at 180iterations finished qdiffx linear iterations at : 17:11:27 total time elapsed so far: 17.46000 # loops : 180 mean,max change (kT/e) : 3.3997002E-04 7.0419312E-03 energy calculations done at 17.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.68000 DelPhi exited at 17:11:28 17.685u 0.491s 0:18.49 98.2% 0+0k 0+0io 0pf+0w