Sat Oct 8 11:52:49 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 8 2011 at 11:52:49 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6375015 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 0.6375015 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 381.3723 centred at (gu) : 89.94854 89.35551 91.05232 assigned negative charge : -383.3306 centred at (gu) : 90.05688 89.24018 91.06378 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6654 nv = 96 ne = 84 npr = 50842 no. pairs analyzed = 50842 no. exposed pairs = 2901 no. arc points = 21287 no. surface atoms = 971 nbur = 1506 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3656 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3600000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2081 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0654224E-09 -4.7126734E-09 midg,1,midg; midg,igrid,midg -1.7363988E-08 8.4118765E-09 1,midg,midg; igrid,midg,midg 9.0724086E-09 -1.4159949E-08 gauss-seidel spectral radius is 0.9872407 estimated iterations to convergence 72 setup time was (sec) 0.7000000 now iterating at: 11:52:50 rms-change max change #iterations 0.1474997 25.11581 at 10iterations 1.4260551E-02 1.893399 at 20iterations 1.3872742E-03 0.1830063 at 30iterations 1.3475158E-04 2.1965027E-02 at 40iterations 1.3382232E-05 2.1057129E-03 at 50iterations finished qdiffx linear iterations at : 11:52:54 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 1.3382232E-05 2.1057129E-03 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 11:52:55 4.761u 0.445s 0:05.50 94.5% 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 11:52:55 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.912505 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 1.912505 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 381.3723 centred at (gu) : 89.84519 88.06618 93.15667 assigned negative charge : -383.3306 centred at (gu) : 90.17056 87.72056 93.19103 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 25236 mr = 50353 m= 3986 mr = 18492 m= 275 mr = 2511 m= 7 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1670 time to turn everything in is 0.7200000 number of dielectric boundary points 30320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 18356 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) : 0.6375015 object centre at (A) : 2.892500 16.95250 29.59400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5147316E-03 -1.4271955E-02 midg,1,midg; midg,igrid,midg -1.3621089E-02 3.9529074E-03 1,midg,midg; igrid,midg,midg 1.6950142E-02 -4.9297187E-02 gauss-seidel spectral radius is 0.9986312 estimated iterations to convergence 214 setup time was (sec) 1.070000 now iterating at: 11:52:56 rms-change max change #iterations 4.273297 175.6089 at 10iterations 1.999384 70.13087 at 20iterations 0.9346210 33.62411 at 30iterations 0.4370108 15.40922 at 40iterations 0.2031309 6.543750 at 50iterations 9.5484592E-02 2.987720 at 60iterations 4.4571716E-02 1.477181 at 70iterations 2.0906614E-02 0.6586795 at 80iterations 9.7437492E-03 0.3001108 at 90iterations 4.5812046E-03 0.1495323 at 100iterations 2.1492508E-03 6.5788269E-02 at 110iterations 1.0019548E-03 3.4025192E-02 at 120iterations finished qdiffx linear iterations at : 11:53:06 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 1.0019548E-03 3.4025192E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 11:53:06 10.757u 0.501s 0:11.54 97.4% 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 Sat Oct 8 2011 at 11:53:06 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.868757 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 2.868757 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 381.3723 centred at (gu) : 89.76766 87.09930 94.73502 assigned negative charge : -383.3306 centred at (gu) : 90.25576 86.58081 94.78661 start vw surface at 0.1500000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 167544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 82466 mr = 122330 m= 29193 mr = 67479 m= 7356 mr = 23215 m= 1253 mr = 5552 m= 102 mr = 878 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 5775 time to turn everything in is 1.880000 number of dielectric boundary points 68416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 18687 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) : 1.912505 object centre at (A) : 2.892500 16.95250 29.59400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4051385E-02 -0.2342707 midg,1,midg; midg,igrid,midg -0.1306654 -1.0876105E-02 1,midg,midg; igrid,midg,midg 0.2289389 -0.8117216 gauss-seidel spectral radius is 0.9992503 estimated iterations to convergence 288 setup time was (sec) 2.240000 now iterating at: 11:53:09 rms-change max change #iterations 9.825603 537.7130 at 10iterations 5.668065 146.8657 at 20iterations 3.248537 58.01283 at 30iterations 1.855742 37.71516 at 40iterations 1.060315 19.99105 at 50iterations 0.6066911 11.59460 at 60iterations 0.3467989 6.461609 at 70iterations 0.1982514 3.770994 at 80iterations 0.1132601 2.190162 at 90iterations 6.4546391E-02 1.161079 at 100iterations 3.6967225E-02 0.6702881 at 110iterations 2.1090876E-02 0.4066782 at 120iterations 1.2050235E-02 0.2153010 at 130iterations 6.8898797E-03 0.1249199 at 140iterations 3.9325282E-03 6.8363190E-02 at 150iterations 2.2480418E-03 3.9920807E-02 at 160iterations 1.2821209E-03 2.2621155E-02 at 170iterations 7.3437550E-04 1.3237000E-02 at 180iterations finished qdiffx linear iterations at : 11:53:24 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 7.3437550E-04 1.3237000E-02 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.11000 DelPhi exited at 11:53:25 18.117u 0.492s 0:18.90 98.4% 0+0k 0+0io 0pf+0w