Sat Oct 15 12:08:55 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 Sat Oct 15 2011 at 12:08:55 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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: 0.5983294 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 0.5983294 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.51403 assigned positive charge : 356.5432 centred at (gu) : 90.54274 89.35699 90.43987 assigned negative charge : -346.0299 centred at (gu) : 90.55066 89.47614 90.41546 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5851 nv = 96 ne = 84 npr = 48377 no. pairs analyzed = 48377 no. exposed pairs = 3282 no. arc points = 23510 no. surface atoms = 1094 nbur = 1334 mkacc time = 7.9999998E-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 = 1.456000 m= 282 mr = 2907 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1639389E-09 5.5009655E-09 midg,1,midg; midg,igrid,midg 9.0984766E-09 4.6370086E-10 1,midg,midg; igrid,midg,midg 3.9767527E-09 4.4980046E-09 gauss-seidel spectral radius is 0.9855382 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 12:08:55 rms-change max change #iterations 0.1013160 18.12754 at 10iterations 8.4979124E-03 1.281508 at 20iterations 7.4042071E-04 0.1169739 at 30iterations 6.9803558E-05 1.0623932E-02 at 40iterations 8.4766652E-06 1.2054443E-03 at 50iterations finished qdiffx linear iterations at : 12:08:58 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.4766652E-06 1.2054443E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 12:08:59 3.466u 0.201s 0:04.08 89.7% 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 Sat Oct 15 2011 at 12:08:59 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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: 1.794988 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 1.794988 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.51403 assigned positive charge : 356.5432 centred at (gu) : 91.62801 88.07057 91.31902 assigned negative charge : -346.0299 centred at (gu) : 91.65190 88.42818 91.24632 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23510 grid for indexing accessible points = 1.400000 m= 20885 mr = 41581 m= 3022 mr = 14387 m= 142 mr = 1738 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 29659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 17905 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) : 0.5983294 object centre at (A) : 26.52300 5.944500 54.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5355588E-02 4.8772369E-02 midg,1,midg; midg,igrid,midg 2.0059247E-02 -5.7248948E-03 1,midg,midg; igrid,midg,midg 3.0761665E-02 3.1196978E-02 gauss-seidel spectral radius is 0.9984622 estimated iterations to convergence 202 setup time was (sec) 0.5200000 now iterating at: 12:09:00 rms-change max change #iterations 3.591315 186.0963 at 10iterations 1.592405 60.41314 at 20iterations 0.7086642 25.60241 at 30iterations 0.3169778 11.72107 at 40iterations 0.1410751 4.901950 at 50iterations 6.3126504E-02 2.369118 at 60iterations 2.8240757E-02 1.091600 at 70iterations 1.2614326E-02 0.4261017 at 80iterations 5.6519564E-03 0.2020836 at 90iterations 2.5170729E-03 9.2075348E-02 at 100iterations 1.1265962E-03 3.9346695E-02 at 110iterations 5.0532067E-04 1.8085480E-02 at 120iterations finished qdiffx linear iterations at : 12:09:07 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 5.0532067E-04 1.8085480E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 12:09:08 7.810u 0.229s 0:08.67 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 Sat Oct 15 2011 at 12:09:08 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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: 2.692482 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 2.692482 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.51403 assigned positive charge : 356.5432 centred at (gu) : 92.44195 87.10585 91.97849 assigned negative charge : -346.0299 centred at (gu) : 92.47783 87.64244 91.86965 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23510 grid for indexing accessible points = 1.400000 m= 68699 mr = 101855 m= 23086 mr = 53796 m= 5286 mr = 17697 m= 694 mr = 3827 m= 34 mr = 393 m= 0 mr = 18 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 66823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 18330 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) : 1.794988 object centre at (A) : 26.52300 5.944500 54.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3143499 0.7675893 midg,1,midg; midg,igrid,midg 0.2373389 -8.3263345E-02 1,midg,midg; igrid,midg,midg 0.3882619 0.3579328 gauss-seidel spectral radius is 0.9992181 estimated iterations to convergence 282 setup time was (sec) 1.020000 now iterating at: 12:09:09 rms-change max change #iterations 8.771200 336.5216 at 10iterations 5.062068 141.0989 at 20iterations 2.914561 64.96338 at 30iterations 1.667322 37.75441 at 40iterations 0.9512880 19.54162 at 50iterations 0.5419291 12.58390 at 60iterations 0.3078532 6.378654 at 70iterations 0.1747770 3.787472 at 80iterations 9.9224083E-02 1.980563 at 90iterations 5.6201767E-02 1.152477 at 100iterations 3.1866450E-02 0.6528931 at 110iterations 1.8095527E-02 0.3908005 at 120iterations 1.0204130E-02 0.2198305 at 130iterations 5.7860618E-03 0.1110296 at 140iterations 3.2745320E-03 6.5014839E-02 at 150iterations 1.8548467E-03 3.8800240E-02 at 160iterations 1.0511567E-03 2.1440983E-02 at 170iterations 5.9689011E-04 1.1539459E-02 at 180iterations finished qdiffx linear iterations at : 12:09:20 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 5.9689011E-04 1.1539459E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 12:09:21 12.540u 0.256s 0:13.14 97.3% 0+0k 0+0io 0pf+0w