Sat Oct 15 12:58:15 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 12:58:15 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 0.6932409 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 0.6932409 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 89.73158 91.36554 90.88615 assigned negative charge : -357.2976 centred at (gu) : 89.71962 91.50537 90.94151 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 47119 no. pairs analyzed = 47119 no. exposed pairs = 2918 no. arc points = 20729 no. surface atoms = 991 nbur = 1374 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4416 m= 0 mr = 86 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3800000 number of dielectric boundary points 3811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2006 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2496676E-08 6.0204739E-09 midg,1,midg; midg,igrid,midg 6.4417463E-08 -4.0164050E-08 1,midg,midg; igrid,midg,midg 2.4375751E-08 3.1275469E-08 gauss-seidel spectral radius is 0.9891899 estimated iterations to convergence 78 setup time was (sec) 0.7500000 now iterating at: 12:58:16 rms-change max change #iterations 0.2004266 33.34425 at 10iterations 2.4354428E-02 3.344952 at 20iterations 3.5459127E-03 0.4754105 at 30iterations 8.1263587E-04 0.1260529 at 40iterations 2.5746721E-04 3.9066315E-02 at 50iterations finished qdiffx linear iterations at : 12:58:20 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 2.5746721E-04 3.9066315E-02 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 12:58:21 4.930u 0.436s 0:05.71 93.8% 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 15 2011 at 12:58:21 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 2.079723 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 2.079723 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 89.19424 94.09634 92.65779 assigned negative charge : -357.2976 centred at (gu) : 89.15865 94.51593 92.82437 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20729 grid for indexing accessible points = 1.400000 m= 31991 mr = 57738 m= 5720 mr = 24068 m= 493 mr = 3716 m= 7 mr = 276 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 313 time to turn everything in is 0.8400000 number of dielectric boundary points 35144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 17634 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) : 0.6932409 object centre at (A) : 18.66650 11.17450 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6554068E-02 1.5430202E-02 midg,1,midg; midg,igrid,midg 1.5844828E-02 -4.2396199E-02 1,midg,midg; igrid,midg,midg 3.6089081E-02 -1.5629573E-02 gauss-seidel spectral radius is 0.9988261 estimated iterations to convergence 231 setup time was (sec) 1.180000 now iterating at: 12:58:22 rms-change max change #iterations 4.846789 207.6747 at 10iterations 2.385303 90.75102 at 20iterations 1.177459 33.76860 at 30iterations 0.5862619 18.35288 at 40iterations 0.2894190 8.566233 at 50iterations 0.1436468 4.233796 at 60iterations 7.1460158E-02 2.072884 at 70iterations 3.5568938E-02 0.9521217 at 80iterations 1.7809961E-02 0.5120847 at 90iterations 9.0137115E-03 0.2626719 at 100iterations 4.6481444E-03 0.1507263 at 110iterations 2.4928430E-03 7.3478699E-02 at 120iterations finished qdiffx linear iterations at : 12:58:33 total time elapsed so far: 11.41000 # loops : 120 mean,max change (kT/e) : 2.4928430E-03 7.3478699E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 12:58:33 11.635u 0.539s 0:12.48 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 15 2011 at 12:58:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 3.119584 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 3.119584 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 88.79134 96.14452 93.98659 assigned negative charge : -357.2976 centred at (gu) : 88.73799 96.77389 94.23656 start vw surface at 0.1400000 fill in re-entrant regions at 1.120000 boundary points on vw surface= 190745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20729 grid for indexing accessible points = 1.400000 m= 100907 mr = 139233 m= 39423 mr = 83557 m= 10377 mr = 32100 m= 2119 mr = 8006 m= 219 mr = 1631 m= 1 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 2.710000 number of dielectric boundary points 79128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.890000 number of grid points assigned charge 17795 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) : 2.079723 object centre at (A) : 18.66650 11.17450 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5347021 1.4456479E-02 midg,1,midg; midg,igrid,midg 0.2643728 -0.4872458 1,midg,midg; igrid,midg,midg 0.3581974 -0.5117778 gauss-seidel spectral radius is 0.9992969 estimated iterations to convergence 298 setup time was (sec) 3.130000 now iterating at: 12:58:37 rms-change max change #iterations 10.85957 480.2267 at 10iterations 6.466001 130.9007 at 20iterations 3.818309 71.31653 at 30iterations 2.253893 41.59020 at 40iterations 1.328929 23.62055 at 50iterations 0.7817274 15.98980 at 60iterations 0.4598595 8.335430 at 70iterations 0.2690383 4.462132 at 80iterations 0.1580111 2.992002 at 90iterations 9.2747666E-02 1.738695 at 100iterations 5.4437812E-02 1.017447 at 110iterations 3.2136817E-02 0.5504608 at 120iterations 1.9130530E-02 0.3683596 at 130iterations 1.1588365E-02 0.1985970 at 140iterations 7.2216499E-03 0.1478882 at 150iterations 4.7089881E-03 0.1040840 at 160iterations 3.2469025E-03 7.0533752E-02 at 170iterations 2.3927030E-03 5.2131653E-02 at 180iterations finished qdiffx linear iterations at : 12:58:55 total time elapsed so far: 20.83000 # loops : 180 mean,max change (kT/e) : 2.3927030E-03 5.2131653E-02 energy calculations done at 20.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.05000 DelPhi exited at 12:58:55 21.056u 0.522s 0:22.02 97.9% 0+0k 0+0io 0pf+0w