Sun Oct 9 15:15:50 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 15:15:50 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: HIR 748 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: 0.4977838 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 0.4977838 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.485959 assigned positive charge : 833.6785 centred at (gu) : 89.73771 89.18290 88.40875 assigned negative charge : -840.1714 centred at (gu) : 89.75877 89.25803 88.36149 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8143 nv = 96 ne = 84 npr = 112117 no. pairs analyzed = 112117 no. exposed pairs = 6452 no. arc points = 44368 no. surface atoms = 2159 nbur = 3282 mkacc time = 0.1900000 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 = 1.708000 m= 279 mr = 4321 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3500000 number of dielectric boundary points 4094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 660 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0551406E-10 1.9231196E-11 midg,1,midg; midg,igrid,midg 9.8322711E-11 -1.4634206E-10 1,midg,midg; igrid,midg,midg -1.5336456E-11 -8.1538144E-11 gauss-seidel spectral radius is 0.9794013 estimated iterations to convergence 58 setup time was (sec) 0.5400000 now iterating at: 15:15:51 rms-change max change #iterations 6.2995441E-02 8.312948 at 10iterations 3.6142815E-03 0.5327284 at 20iterations 3.2539942E-04 5.1938057E-02 at 30iterations 5.9863920E-05 8.2802773E-03 at 40iterations 1.3131683E-05 1.7929077E-03 at 50iterations finished qdiffx linear iterations at : 15:15:54 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.3131683E-05 1.7929077E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 15:15:54 3.563u 0.171s 0:04.01 93.0% 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 15:15:54 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: HIR 748 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: 1.493351 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 1.493351 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.485959 assigned positive charge : 833.6785 centred at (gu) : 89.21133 87.54728 85.22493 assigned negative charge : -840.1714 centred at (gu) : 89.27636 87.77407 85.08466 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 93642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44368 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 25900 mr = 65318 m= 2088 mr = 17340 m= 31 mr = 834 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4249 time to turn everything in is 0.4500000 number of dielectric boundary points 38169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 39273 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) : 0.4977838 object centre at (A) : 17.23450 130.4940 0.9145002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8517957E-03 -4.7243964E-03 midg,1,midg; midg,igrid,midg 1.1039745E-02 -1.2796992E-02 1,midg,midg; igrid,midg,midg -2.0226473E-02 -4.4502928E-03 gauss-seidel spectral radius is 0.9980460 estimated iterations to convergence 180 setup time was (sec) 0.6600000 now iterating at: 15:15:55 rms-change max change #iterations 3.902717 164.3611 at 10iterations 1.574715 51.91356 at 20iterations 0.6335852 20.96418 at 30iterations 0.2568414 8.030735 at 40iterations 0.1036996 3.455558 at 50iterations 4.2069703E-02 1.318996 at 60iterations 1.7071551E-02 0.5663600 at 70iterations 6.8860510E-03 0.2196198 at 80iterations 2.8007780E-03 9.5203400E-02 at 90iterations 1.1319702E-03 3.8166046E-02 at 100iterations 4.6059943E-04 1.4421701E-02 at 110iterations 1.8891810E-04 6.2727928E-03 at 120iterations finished qdiffx linear iterations at : 15:16:02 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.8891810E-04 6.2727928E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 15:16:02 7.850u 0.204s 0:08.39 95.9% 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 Sun Oct 9 2011 at 15:16:02 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: HIR 748 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: 2.240027 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 2.240027 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.485959 assigned positive charge : 833.6785 centred at (gu) : 88.81630 86.32027 82.83678 assigned negative charge : -840.1714 centred at (gu) : 88.91438 86.66117 82.62697 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 219154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44368 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 94739 mr = 161146 m= 22838 mr = 74195 m= 2819 mr = 16407 m= 116 mr = 1673 m= 0 mr = 28 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 14750 time to turn everything in is 1.080000 number of dielectric boundary points 86217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 42009 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) : 1.493351 object centre at (A) : 17.23450 130.4940 0.9145002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0934941E-02 -0.1271470 midg,1,midg; midg,igrid,midg 0.2229089 -0.2768333 1,midg,midg; igrid,midg,midg -0.2999095 2.1672463E-02 gauss-seidel spectral radius is 0.9991453 estimated iterations to convergence 270 setup time was (sec) 1.320000 now iterating at: 15:16:04 rms-change max change #iterations 10.65261 258.9047 at 10iterations 6.015632 153.2700 at 20iterations 3.377056 84.77539 at 30iterations 1.887551 40.93898 at 40iterations 1.049606 21.70313 at 50iterations 0.5831230 12.85750 at 60iterations 0.3229499 6.762951 at 70iterations 0.1792054 3.290031 at 80iterations 9.8860331E-02 1.876711 at 90iterations 5.4619391E-02 0.9998007 at 100iterations 3.0186823E-02 0.5631304 at 110iterations 1.6670665E-02 0.2701168 at 120iterations 9.2027532E-03 0.1595688 at 130iterations 5.0619342E-03 9.0957642E-02 at 140iterations 2.7917421E-03 5.0596237E-02 at 150iterations 1.5434162E-03 2.8766632E-02 at 160iterations 8.5144956E-04 1.4802933E-02 at 170iterations 4.6869868E-04 8.5592270E-03 at 180iterations finished qdiffx linear iterations at : 15:16:15 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 4.6869868E-04 8.5592270E-03 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 15:16:16 12.951u 0.208s 0:13.44 97.8% 0+0k 0+0io 0pf+0w