Tue Oct 11 05:29:58 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 Tue Oct 11 2011 at 05:29:58 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6791042 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 0.6791042 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 90.58183 90.28371 89.67422 assigned negative charge : -312.6442 centred at (gu) : 90.71170 90.28070 89.74258 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6495 nv = 96 ne = 84 npr = 42103 no. pairs analyzed = 42103 no. exposed pairs = 2557 no. arc points = 17386 no. surface atoms = 872 nbur = 1418 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 3724 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1744 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7928914E-08 9.2952046E-09 midg,1,midg; midg,igrid,midg 2.5286765E-08 2.9880805E-08 1,midg,midg; igrid,midg,midg 5.3696375E-08 -7.2884387E-09 gauss-seidel spectral radius is 0.9887058 estimated iterations to convergence 77 setup time was (sec) 0.4600000 now iterating at: 05:29:58 rms-change max change #iterations 0.1695429 26.88825 at 10iterations 1.9237535E-02 2.974983 at 20iterations 2.4888995E-03 0.3294632 at 30iterations 4.1938919E-04 5.5320740E-02 at 40iterations 1.0631138E-04 1.2456894E-02 at 50iterations finished qdiffx linear iterations at : 05:30:01 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.0631138E-04 1.2456894E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 05:30:01 3.070u 0.130s 0:03.59 89.1% 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 Tue Oct 11 2011 at 05:30:02 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.037313 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 2.037313 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 91.74568 90.85095 89.02257 assigned negative charge : -312.6442 centred at (gu) : 92.13533 90.84214 89.22799 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17386 grid for indexing accessible points = 1.400000 m= 27339 mr = 49437 m= 4944 mr = 20646 m= 399 mr = 3186 m= 8 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 28691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15565 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) : 0.6791042 object centre at (A) : 24.30500 21.08800 23.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4869147E-02 5.2956201E-02 midg,1,midg; midg,igrid,midg 4.7236695E-03 2.2393500E-02 1,midg,midg; igrid,midg,midg 2.7047720E-02 2.8154426E-04 gauss-seidel spectral radius is 0.9987432 estimated iterations to convergence 223 setup time was (sec) 0.8000000 now iterating at: 05:30:03 rms-change max change #iterations 4.284406 179.4494 at 10iterations 2.072399 68.50752 at 20iterations 1.005642 35.49476 at 30iterations 0.4845935 16.05079 at 40iterations 0.2352422 7.606348 at 50iterations 0.1140162 3.911032 at 60iterations 5.5318255E-02 1.632794 at 70iterations 2.6907567E-02 0.9179049 at 80iterations 1.3110584E-02 0.4237404 at 90iterations 6.4209085E-03 0.2130117 at 100iterations 3.1894930E-03 9.7667694E-02 at 110iterations 1.6299451E-03 5.8594227E-02 at 120iterations finished qdiffx linear iterations at : 05:30:09 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.6299451E-03 5.8594227E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 05:30:10 7.619u 0.232s 0:08.13 96.4% 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 Tue Oct 11 2011 at 05:30:10 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.055969 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 3.055969 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 92.61853 91.27658 88.53375 assigned negative charge : -312.6442 centred at (gu) : 93.20306 91.26334 88.84202 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17386 grid for indexing accessible points = 1.400000 m= 86232 mr = 118902 m= 33973 mr = 71698 m= 9226 mr = 27731 m= 1587 mr = 6985 m= 133 mr = 1106 m= 8 mr = 61 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 64715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15751 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) : 2.037313 object centre at (A) : 24.30500 21.08800 23.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3462380 0.7477610 midg,1,midg; midg,igrid,midg 8.1326161E-03 0.2025723 1,midg,midg; igrid,midg,midg 0.2325315 4.3511923E-02 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 05:30:12 rms-change max change #iterations 9.758031 310.6889 at 10iterations 5.729015 144.7894 at 20iterations 3.364226 97.01910 at 30iterations 1.966186 43.22805 at 40iterations 1.145286 24.23606 at 50iterations 0.6687765 12.69481 at 60iterations 0.3888256 7.478558 at 70iterations 0.2261848 4.594005 at 80iterations 0.1313603 2.377290 at 90iterations 7.6313846E-02 1.592054 at 100iterations 4.4330023E-02 0.7957277 at 110iterations 2.5862716E-02 0.5076904 at 120iterations 1.5134813E-02 0.2769966 at 130iterations 8.9742132E-03 0.1724358 at 140iterations 5.4084132E-03 0.1145821 at 150iterations 3.3742453E-03 6.2217712E-02 at 160iterations 2.2026675E-03 3.9730072E-02 at 170iterations 1.5262843E-03 2.8526306E-02 at 180iterations finished qdiffx linear iterations at : 05:30:22 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 1.5262843E-03 2.8526306E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 05:30:23 12.529u 0.241s 0:13.06 97.7% 0+0k 0+0io 0pf+0w