Mon Oct 10 17:04:35 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 17:04:36 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIT 1107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5732228 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 0.5732228 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4859793 assigned positive charge : 423.4163 centred at (gu) : 89.79301 89.31623 89.38634 assigned negative charge : -423.9033 centred at (gu) : 89.78862 89.18516 89.21872 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5822 nv = 96 ne = 84 npr = 56445 no. pairs analyzed = 56445 no. exposed pairs = 3611 no. arc points = 25658 no. surface atoms = 1219 nbur = 1568 mkacc time = 9.9999994E-02 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 = 1.512000 m= 263 mr = 2896 m= 0 mr = 19 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2628 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3661562E-09 2.3318645E-09 midg,1,midg; midg,igrid,midg -2.6766562E-09 1.7929589E-09 1,midg,midg; igrid,midg,midg -1.2236598E-10 2.8392233E-11 gauss-seidel spectral radius is 0.9842802 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 17:04:36 rms-change max change #iterations 9.2479087E-02 18.34910 at 10iterations 7.1320380E-03 1.167496 at 20iterations 5.5647944E-04 8.2191467E-02 at 30iterations 4.6015433E-05 7.1163177E-03 at 40iterations 4.8741836E-06 8.6593628E-04 at 50iterations finished qdiffx linear iterations at : 17:04:39 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 4.8741836E-06 8.6593628E-04 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 17:04:40 3.535u 0.200s 0:04.11 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 Mon Oct 10 2011 at 17:04:40 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIT 1107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.719668 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 1.719668 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4859793 assigned positive charge : 423.4163 centred at (gu) : 89.37816 87.94778 88.15829 assigned negative charge : -423.9033 centred at (gu) : 89.36546 87.55532 87.65575 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25658 grid for indexing accessible points = 1.400000 m= 19904 mr = 42471 m= 2258 mr = 13571 m= 58 mr = 1047 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 159 time to turn everything in is 0.3300000 number of dielectric boundary points 29414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20458 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) : 0.5732228 object centre at (A) : 15.96650 35.83700 20.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1571787E-02 1.0514848E-02 midg,1,midg; midg,igrid,midg -5.8407160E-03 5.2786767E-03 1,midg,midg; igrid,midg,midg 9.6092734E-04 6.7264992E-03 gauss-seidel spectral radius is 0.9983489 estimated iterations to convergence 195 setup time was (sec) 0.5600000 now iterating at: 17:04:40 rms-change max change #iterations 3.609487 166.3285 at 10iterations 1.557618 61.47091 at 20iterations 0.6743912 26.93390 at 30iterations 0.2934389 10.38534 at 40iterations 0.1272586 4.720531 at 50iterations 5.5073239E-02 2.193684 at 60iterations 2.3885045E-02 0.9017224 at 70iterations 1.0369909E-02 0.4235840 at 80iterations 4.4917366E-03 0.1528168 at 90iterations 1.9450260E-03 6.9561005E-02 at 100iterations 8.4906368E-04 2.8686523E-02 at 110iterations 3.6788979E-04 1.3824463E-02 at 120iterations finished qdiffx linear iterations at : 17:04:49 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 3.6788979E-04 1.3824463E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 17:04:49 8.788u 0.222s 0:09.42 95.5% 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 17:04:49 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIT 1107 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.579503 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 2.579503 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4859793 assigned positive charge : 423.4163 centred at (gu) : 89.06691 86.92148 87.23703 assigned negative charge : -423.9033 centred at (gu) : 89.04819 86.33286 86.48362 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 149086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25658 grid for indexing accessible points = 1.400000 m= 67786 mr = 104296 m= 20606 mr = 52883 m= 3501 mr = 15380 m= 269 mr = 2202 m= 8 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 453 time to turn everything in is 0.8000000 number of dielectric boundary points 66376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21154 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) : 1.719668 object centre at (A) : 15.96650 35.83700 20.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2349780 0.1599581 midg,1,midg; midg,igrid,midg -5.4747436E-02 6.6296153E-02 1,midg,midg; igrid,midg,midg 3.9715245E-02 0.2752921 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.050000 now iterating at: 17:04:50 rms-change max change #iterations 9.243724 345.6142 at 10iterations 5.278030 135.2839 at 20iterations 3.006631 71.81224 at 30iterations 1.697886 41.50416 at 40iterations 0.9592301 24.94987 at 50iterations 0.5389109 12.53956 at 60iterations 0.3033920 6.267399 at 70iterations 0.1703367 3.723873 at 80iterations 9.5455416E-02 2.054653 at 90iterations 5.3599644E-02 1.117395 at 100iterations 2.9995915E-02 0.6363564 at 110iterations 1.6792430E-02 0.3347092 at 120iterations 9.4269505E-03 0.1949768 at 130iterations 5.2717994E-03 0.1121187 at 140iterations 2.9519063E-03 6.3732147E-02 at 150iterations 1.6492787E-03 3.4904480E-02 at 160iterations 9.2581462E-04 1.9581795E-02 at 170iterations 5.1640824E-04 1.1142731E-02 at 180iterations finished qdiffx linear iterations at : 17:05:02 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 5.1640824E-04 1.1142731E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 17:05:03 13.003u 0.221s 0:14.17 93.2% 0+0k 0+0io 0pf+0w