Sat Oct 8 11:38:56 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 11:38:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 0.5974658 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 0.5974658 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999991 assigned positive charge : 413.6221 centred at (gu) : 90.33312 89.51902 91.09892 assigned negative charge : -416.6230 centred at (gu) : 90.40551 89.51404 91.12575 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6647 nv = 96 ne = 84 npr = 56461 no. pairs analyzed = 56461 no. exposed pairs = 3703 no. arc points = 25935 no. surface atoms = 1247 nbur = 1551 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3367 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2602 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8358 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5983272E-10 -2.7353395E-09 midg,1,midg; midg,igrid,midg -1.4891408E-09 -8.8079938E-10 1,midg,midg; igrid,midg,midg 1.3264633E-09 -4.0982657E-09 gauss-seidel spectral radius is 0.9855250 estimated iterations to convergence 68 setup time was (sec) 0.7200000 now iterating at: 11:38:57 rms-change max change #iterations 0.1144371 15.97715 at 10iterations 9.7427210E-03 1.468711 at 20iterations 8.7998551E-04 0.1149611 at 30iterations 1.2325452E-04 1.7303467E-02 at 40iterations 3.3090932E-05 4.2572021E-03 at 50iterations finished qdiffx linear iterations at : 11:39:01 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 3.3090932E-05 4.2572021E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:39:02 4.482u 0.404s 0:05.75 84.8% 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 11:39:02 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 1.792397 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 1.792397 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999991 assigned positive charge : 413.6221 centred at (gu) : 90.99842 88.55598 93.29595 assigned negative charge : -416.6230 centred at (gu) : 91.21613 88.54173 93.37673 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 72877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25935 grid for indexing accessible points = 1.400000 m= 23189 mr = 48648 m= 2901 mr = 15935 m= 113 mr = 1474 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.7300000 number of dielectric boundary points 33011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20667 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) : 0.5974658 object centre at (A) : -30.30400 17.76450 -18.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2854257E-03 -2.7300147E-03 midg,1,midg; midg,igrid,midg -2.2540325E-02 9.8585729E-03 1,midg,midg; igrid,midg,midg -1.4251778E-03 -1.1196741E-02 gauss-seidel spectral radius is 0.9984914 estimated iterations to convergence 204 setup time was (sec) 1.050000 now iterating at: 11:39:04 rms-change max change #iterations 3.905714 158.9919 at 10iterations 1.751775 66.81940 at 20iterations 0.7861152 28.44166 at 30iterations 0.3534724 11.41425 at 40iterations 0.1586504 5.519211 at 50iterations 7.1753554E-02 2.504662 at 60iterations 3.2150220E-02 1.094670 at 70iterations 1.4473500E-02 0.4894114 at 80iterations 6.5557589E-03 0.2219925 at 90iterations 2.9622978E-03 9.5825195E-02 at 100iterations 1.3412707E-03 4.4862747E-02 at 110iterations 6.1546214E-04 1.9086838E-02 at 120iterations finished qdiffx linear iterations at : 11:39:13 total time elapsed so far: 10.10000 # loops : 120 mean,max change (kT/e) : 6.1546214E-04 1.9086838E-02 energy calculations done at 10.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 11:39:13 10.331u 0.454s 0:11.31 95.3% 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 11:39:13 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 2.688596 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 2.688596 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999991 assigned positive charge : 413.6221 centred at (gu) : 91.49760 87.83379 94.94370 assigned negative charge : -416.6230 centred at (gu) : 91.82406 87.81258 95.06505 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 168989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25935 grid for indexing accessible points = 1.400000 m= 78032 mr = 119091 m= 24267 mr = 61242 m= 4785 mr = 18353 m= 443 mr = 3240 m= 11 mr = 222 m= 0 mr = 4 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 369 time to turn everything in is 1.840000 number of dielectric boundary points 74375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 21164 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) : 1.792397 object centre at (A) : -30.30400 17.76450 -18.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1547584 -2.5670422E-02 midg,1,midg; midg,igrid,midg -0.3197682 0.3511458 1,midg,midg; igrid,midg,midg -4.6788443E-02 -0.1547533 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 2.210000 now iterating at: 11:39:16 rms-change max change #iterations 9.689338 335.9456 at 10iterations 5.760685 135.4744 at 20iterations 3.368980 81.75430 at 30iterations 1.959080 41.72285 at 40iterations 1.135666 26.53705 at 50iterations 0.6534717 13.68177 at 60iterations 0.3775448 8.235416 at 70iterations 0.2165109 4.239870 at 80iterations 0.1244186 2.551636 at 90iterations 7.1291029E-02 1.524540 at 100iterations 4.0786687E-02 0.8738337 at 110iterations 2.3293778E-02 0.4646788 at 120iterations 1.3303937E-02 0.2490265 at 130iterations 7.6048514E-03 0.1403999 at 140iterations 4.3595410E-03 9.0110779E-02 at 150iterations 2.4942481E-03 5.0009012E-02 at 160iterations 1.4332216E-03 2.8774500E-02 at 170iterations 8.2551420E-04 1.5945435E-02 at 180iterations finished qdiffx linear iterations at : 11:39:31 total time elapsed so far: 17.44000 # loops : 180 mean,max change (kT/e) : 8.2551420E-04 1.5945435E-02 energy calculations done at 17.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.66000 DelPhi exited at 11:39:33 17.664u 0.484s 0:19.08 95.0% 0+0k 0+0io 0pf+0w