Sun Oct 9 01:48:14 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+sph.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 = amb.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 01:48:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5358782 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 0.5358782 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3273 net assigned charge : 16.50003 assigned positive charge : 504.0574 centred at (gu) : 89.85339 89.66129 90.13534 assigned negative charge : -487.5593 centred at (gu) : 89.78683 89.66710 90.32110 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6632 nv = 96 ne = 84 npr = 64883 no. pairs analyzed = 64883 no. exposed pairs = 4749 no. arc points = 33633 no. surface atoms = 1571 nbur = 1844 mkacc time = 0.1400000 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 = 1.568000 m= 301 mr = 3211 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3324 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5374352E-09 -2.6434030E-10 midg,1,midg; midg,igrid,midg 7.8121687E-10 6.0890110E-10 1,midg,midg; igrid,midg,midg 3.6934153E-10 9.8130859E-10 gauss-seidel spectral radius is 0.9821045 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 01:48:14 rms-change max change #iterations 7.0912547E-02 10.88643 at 10iterations 4.4941986E-03 0.6669998 at 20iterations 3.1264249E-04 5.4010391E-02 at 30iterations 3.2808832E-05 5.2733421E-03 at 40iterations 5.6206013E-06 8.9931488E-04 at 50iterations finished qdiffx linear iterations at : 01:48:17 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 5.6206013E-06 8.9931488E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 01:48:17 3.186u 0.129s 0:03.74 88.2% 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 01:48:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.607635 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 1.607635 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3273 net assigned charge : 16.50003 assigned positive charge : 504.0574 centred at (gu) : 89.55897 88.98310 90.40528 assigned negative charge : -487.5593 centred at (gu) : 89.36019 89.00105 90.96289 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33633 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23106 mr = 48312 m= 2389 mr = 15442 m= 67 mr = 1089 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.5200000 number of dielectric boundary points 34433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 398 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 25003 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) : 0.5358782 object centre at (A) : -19.96450 209.9160 112.3505 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1639903E-02 -1.1847135E-02 midg,1,midg; midg,igrid,midg 2.5895165E-02 2.0233130E-02 1,midg,midg; igrid,midg,midg 1.0035271E-02 1.2305868E-02 gauss-seidel spectral radius is 0.9981971 estimated iterations to convergence 187 setup time was (sec) 0.7800000 now iterating at: 01:48:18 rms-change max change #iterations 3.388650 141.3675 at 10iterations 1.407561 58.94273 at 20iterations 0.5889770 18.91797 at 30iterations 0.2452166 8.875767 at 40iterations 0.1017936 3.315639 at 50iterations 4.2532567E-02 1.513101 at 60iterations 1.7779225E-02 0.5995531 at 70iterations 7.4309353E-03 0.2847167 at 80iterations 3.1019375E-03 0.1118088 at 90iterations 1.2973970E-03 4.1301727E-02 at 100iterations 5.4461427E-04 2.1144867E-02 at 110iterations 2.2861107E-04 7.9498291E-03 at 120iterations finished qdiffx linear iterations at : 01:48:24 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 2.2861107E-04 7.9498291E-03 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 01:48:25 6.938u 0.167s 0:07.43 95.4% 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 01:48:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 2.411452 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 2.411452 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3273 net assigned charge : 16.50003 assigned positive charge : 504.0574 centred at (gu) : 89.33821 88.47437 90.60749 assigned negative charge : -487.5593 centred at (gu) : 89.04005 88.50137 91.44420 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 171125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33633 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78598 mr = 118833 m= 22876 mr = 60639 m= 3572 mr = 16853 m= 209 mr = 2235 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1038 time to turn everything in is 1.190000 number of dielectric boundary points 77757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 26149 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) : 1.607635 object centre at (A) : -19.96450 209.9160 112.3505 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1882176 -0.1392389 midg,1,midg; midg,igrid,midg 0.3452040 0.3520075 1,midg,midg; igrid,midg,midg 0.1553146 0.1316356 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 1.480000 now iterating at: 01:48:27 rms-change max change #iterations 8.912226 260.5023 at 10iterations 5.089410 137.4323 at 20iterations 2.888900 67.50479 at 30iterations 1.628706 34.08160 at 40iterations 0.9137272 18.38200 at 50iterations 0.5115103 12.91275 at 60iterations 0.2861927 5.685230 at 70iterations 0.1590981 3.441788 at 80iterations 8.8670269E-02 1.779633 at 90iterations 4.9394771E-02 0.9548264 at 100iterations 2.7432945E-02 0.5703964 at 110iterations 1.5267651E-02 0.2933712 at 120iterations 8.4729213E-03 0.1629410 at 130iterations 4.6979091E-03 8.6228848E-02 at 140iterations 2.6040762E-03 5.3394556E-02 at 150iterations 1.4466337E-03 2.8184891E-02 at 160iterations 8.0328289E-04 1.6849995E-02 at 170iterations 4.4567737E-04 8.5296631E-03 at 180iterations finished qdiffx linear iterations at : 01:48:36 total time elapsed so far: 10.90000 # loops : 180 mean,max change (kT/e) : 4.4567737E-04 8.5296631E-03 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 01:48:37 11.075u 0.180s 0:11.85 94.9% 0+0k 0+0io 0pf+0w