Sun Oct 9 03:47:41 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+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 Sun Oct 9 2011 at 03:47:41 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4094778 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 0.4094778 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.31400 assigned positive charge : 694.7480 centred at (gu) : 85.72368 91.66469 83.54082 assigned negative charge : -673.4390 centred at (gu) : 85.55183 91.73233 83.44848 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 4576 nv = 96 ne = 84 npr = 96221 no. pairs analyzed = 96221 no. exposed pairs = 6189 no. arc points = 43014 no. surface atoms = 2081 nbur = 2663 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 = 2.044000 m= 104 mr = 2012 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 2668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 719 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 6163 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4125648E-12 2.7991685E-13 midg,1,midg; midg,igrid,midg 1.0784348E-12 8.0908907E-13 1,midg,midg; igrid,midg,midg -2.6918699E-12 7.3532077E-13 gauss-seidel spectral radius is 0.9696528 estimated iterations to convergence 48 setup time was (sec) 0.7000000 now iterating at: 03:47:42 rms-change max change #iterations 2.1984905E-02 4.684776 at 10iterations 2.4489469E-03 0.4571486 at 20iterations 6.9632870E-04 0.1304169 at 30iterations 2.0499456E-04 3.8225174E-02 at 40iterations 6.0677623E-05 1.1478424E-02 at 50iterations finished qdiffx linear iterations at : 03:47:45 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 6.0677623E-05 1.1478424E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 03:47:45 3.637u 0.199s 0:04.12 92.7% 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 Sun Oct 9 2011 at 03:47:45 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.228433 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 1.228433 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.31400 assigned positive charge : 694.7480 centred at (gu) : 77.16939 94.99275 70.62067 assigned negative charge : -673.4390 centred at (gu) : 76.65514 95.19701 70.34514 start vw surface at 0.1900000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 53682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.904000 m= 11088 mr = 33472 m= 415 mr = 6309 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.4600000 number of dielectric boundary points 25355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 796 ## 37 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 29818 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) : 0.4094778 object centre at (A) : 38.29950 21.54450 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2028742E-02 1.4275638E-03 midg,1,midg; midg,igrid,midg 1.9533464E-03 1.0578635E-03 1,midg,midg; igrid,midg,midg -6.9121015E-04 1.2146845E-03 gauss-seidel spectral radius is 0.9968063 estimated iterations to convergence 141 setup time was (sec) 0.7500000 now iterating at: 03:47:46 rms-change max change #iterations 2.094213 111.0761 at 10iterations 0.6513321 28.39709 at 20iterations 0.2049588 8.647326 at 30iterations 6.5363131E-02 3.347389 at 40iterations 2.1076519E-02 0.9274797 at 50iterations 7.5148405E-03 0.3430243 at 60iterations 3.3155421E-03 0.1613293 at 70iterations 1.8687210E-03 7.9690933E-02 at 80iterations 1.1955155E-03 5.0319672E-02 at 90iterations 7.9477637E-04 3.3147812E-02 at 100iterations 5.3375104E-04 2.2462845E-02 at 110iterations 3.5936534E-04 1.5211105E-02 at 120iterations finished qdiffx linear iterations at : 03:47:53 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 3.5936534E-04 1.5211105E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 03:47:54 7.643u 0.243s 0:08.34 94.4% 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 Sun Oct 9 2011 at 03:47:54 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: 352 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.842650 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 1.842650 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.31400 assigned positive charge : 694.7480 centred at (gu) : 70.75367 97.48884 60.93063 assigned negative charge : -673.4390 centred at (gu) : 69.98261 97.79547 60.51767 start vw surface at 0.1900000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 126007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 44046 mr = 84290 m= 6807 mr = 31355 m= 309 mr = 4109 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 256 time to turn everything in is 0.9700000 number of dielectric boundary points 57351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 34713 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) : 1.228433 object centre at (A) : 38.29950 21.54450 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4335794 2.1592341E-02 midg,1,midg; midg,igrid,midg 4.8600271E-02 2.1372719E-02 1,midg,midg; igrid,midg,midg 3.4958557E-03 1.7339712E-02 gauss-seidel spectral radius is 0.9986199 estimated iterations to convergence 213 setup time was (sec) 1.290000 now iterating at: 03:47:55 rms-change max change #iterations 6.534507 254.3810 at 10iterations 3.175626 101.3852 at 20iterations 1.529109 49.74663 at 30iterations 0.7334744 20.74228 at 40iterations 0.3485544 9.410271 at 50iterations 0.1647878 4.358722 at 60iterations 7.8319691E-02 2.182775 at 70iterations 3.7082385E-02 0.9889092 at 80iterations 1.7522920E-02 0.4492416 at 90iterations 8.3109038E-03 0.2204230 at 100iterations 3.9589670E-03 9.8182678E-02 at 110iterations 1.9136836E-03 5.3411484E-02 at 120iterations 9.5922389E-04 2.8205872E-02 at 130iterations 5.1383744E-04 1.4783859E-02 at 140iterations 3.0088119E-04 8.8043213E-03 at 150iterations 1.9498651E-04 5.4454803E-03 at 160iterations 1.3556922E-04 3.6506653E-03 at 170iterations 9.8566808E-05 2.4776459E-03 at 180iterations finished qdiffx linear iterations at : 03:48:06 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 9.8566808E-05 2.4776459E-03 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 03:48:06 12.139u 0.263s 0:12.68 97.7% 0+0k 0+0io 0pf+0w