Sat Oct 8 13:31:18 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 13:31:18 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: GLU 644 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5276028 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): -4.855000 62.62000 ymin,ymax (A): -61.36200 2.140000 zmin,zma (A): -30.12400 22.11300 x,y,z range (A): 67.47501 63.50200 52.23700 scale (grids/A): 0.5276028 object centre (A): 28.88250 -29.61100 -4.005501 number of atom coordinates read : 3687 total number of charged atoms : 3539 net assigned charge : 1.226027 assigned positive charge : 556.6279 centred at (gu) : 90.69975 90.42861 90.26858 assigned negative charge : -555.4037 centred at (gu) : 90.64174 90.26724 90.36082 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 73805 no. pairs analyzed = 73805 no. exposed pairs = 4801 no. arc points = 33769 no. surface atoms = 1600 nbur = 2087 mkacc time = 0.2000000 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= 246 mr = 3419 m= 0 mr = 10 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3339 ## 487 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7773584E-10 -3.7277928E-10 midg,1,midg; midg,igrid,midg -5.7144911E-10 7.5742029E-10 1,midg,midg; igrid,midg,midg -1.7091169E-10 3.2127201E-10 gauss-seidel spectral radius is 0.9815463 estimated iterations to convergence 61 setup time was (sec) 0.7100000 now iterating at: 13:31:19 rms-change max change #iterations 6.9455147E-02 11.73088 at 10iterations 5.6017148E-03 0.9528160 at 20iterations 1.7710847E-03 0.3142948 at 30iterations 8.4415165E-04 0.1515999 at 40iterations 4.0528100E-04 7.3244095E-02 at 50iterations finished qdiffx linear iterations at : 13:31:23 total time elapsed so far: 5.110000 # loops : 50 mean,max change (kT/e) : 4.0528100E-04 7.3244095E-02 energy calculations done at 5.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.280000 DelPhi exited at 13:31:24 5.281u 0.450s 0:06.04 94.8% 0+0k 0+0io 6pf+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 13:31:24 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: GLU 644 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.582808 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): -4.855000 62.62000 ymin,ymax (A): -61.36200 2.140000 zmin,zma (A): -30.12400 22.11300 x,y,z range (A): 67.47501 63.50200 52.23700 scale (grids/A): 1.582808 object centre (A): 28.88250 -29.61100 -4.005501 number of atom coordinates read : 3687 total number of charged atoms : 3539 net assigned charge : 1.226027 assigned positive charge : 556.6279 centred at (gu) : 92.09815 91.28465 90.80503 assigned negative charge : -555.4037 centred at (gu) : 91.92466 90.80137 91.08213 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22132 mr = 50265 m= 2179 mr = 14916 m= 63 mr = 987 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 699 time to turn everything in is 0.6400000 number of dielectric boundary points 32283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 485 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 26859 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) : 0.5276028 object centre at (A) : 28.88250 -29.61100 -4.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1094346E-03 -8.5405689E-03 midg,1,midg; midg,igrid,midg 4.8228069E-03 1.2036258E-02 1,midg,midg; igrid,midg,midg 1.0144538E-03 9.5778033E-03 gauss-seidel spectral radius is 0.9981459 estimated iterations to convergence 185 setup time was (sec) 1.000000 now iterating at: 13:31:25 rms-change max change #iterations 3.498698 160.9387 at 10iterations 1.444877 54.32880 at 20iterations 0.5973736 20.94538 at 30iterations 0.2487389 9.107497 at 40iterations 0.1024349 3.711332 at 50iterations 4.2856324E-02 1.559850 at 60iterations 1.8194936E-02 0.6607084 at 70iterations 8.1250118E-03 0.2945337 at 80iterations 4.1100420E-03 0.1619263 at 90iterations 2.4797313E-03 9.7953796E-02 at 100iterations 1.7206648E-03 6.3770294E-02 at 110iterations 1.2751771E-03 4.7132492E-02 at 120iterations finished qdiffx linear iterations at : 13:31:36 total time elapsed so far: 12.22000 # loops : 120 mean,max change (kT/e) : 1.2751771E-03 4.7132492E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 13:31:37 12.417u 0.524s 0:13.25 97.5% 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 Sat Oct 8 2011 at 13:31:37 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: GLU 644 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.374213 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): -4.855000 62.62000 ymin,ymax (A): -61.36200 2.140000 zmin,zma (A): -30.12400 22.11300 x,y,z range (A): 67.47501 63.50200 52.23700 scale (grids/A): 2.374213 object centre (A): 28.88250 -29.61100 -4.005501 number of atom coordinates read : 3687 total number of charged atoms : 3539 net assigned charge : 1.226027 assigned positive charge : 556.6279 centred at (gu) : 93.14695 91.92697 91.20734 assigned negative charge : -555.4037 centred at (gu) : 92.88692 91.20177 91.62328 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 171960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 77644 mr = 122926 m= 21163 mr = 60763 m= 3268 mr = 15614 m= 271 mr = 2058 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2252 time to turn everything in is 1.580000 number of dielectric boundary points 72834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 28254 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) : 1.582808 object centre at (A) : 28.88250 -29.61100 -4.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8366877E-03 -9.5395029E-02 midg,1,midg; midg,igrid,midg 0.2148687 0.1042788 1,midg,midg; igrid,midg,midg -1.0642853E-02 0.3006138 gauss-seidel spectral radius is 0.9991505 estimated iterations to convergence 271 setup time was (sec) 2.020000 now iterating at: 13:31:40 rms-change max change #iterations 9.411903 378.4290 at 10iterations 5.361789 126.5981 at 20iterations 3.029242 80.28493 at 30iterations 1.708021 40.05093 at 40iterations 0.9568689 24.42606 at 50iterations 0.5360135 12.53340 at 60iterations 0.2993011 7.461987 at 70iterations 0.1666766 3.809017 at 80iterations 9.2771202E-02 2.033548 at 90iterations 5.1723979E-02 1.133059 at 100iterations 2.8775996E-02 0.6434031 at 110iterations 1.5985740E-02 0.3812923 at 120iterations 8.9285914E-03 0.2093210 at 130iterations 5.0338809E-03 0.1046181 at 140iterations 2.8829772E-03 7.1869016E-02 at 150iterations 1.7141422E-03 3.8221359E-02 at 160iterations 1.0867664E-03 2.5411606E-02 at 170iterations 7.4813870E-04 1.9851685E-02 at 180iterations finished qdiffx linear iterations at : 13:31:58 total time elapsed so far: 20.78000 # loops : 180 mean,max change (kT/e) : 7.4813870E-04 1.9851685E-02 energy calculations done at 20.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.94000 DelPhi exited at 13:31:59 20.950u 0.550s 0:21.77 98.7% 0+0k 0+0io 0pf+0w