Sun Oct 9 23:22:44 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 23:22:44 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 = 2266 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: 0.6686575 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 0.6686575 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 334.5995 centred at (gu) : 91.79980 91.06586 90.18591 assigned negative charge : -333.0998 centred at (gu) : 91.74915 90.93084 89.96118 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7021 nv = 96 ne = 84 npr = 44507 no. pairs analyzed = 44507 no. exposed pairs = 2976 no. arc points = 21136 no. surface atoms = 1011 nbur = 1255 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3712 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1969 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2535682E-08 5.2428444E-08 midg,1,midg; midg,igrid,midg -1.9662137E-08 4.0305849E-08 1,midg,midg; igrid,midg,midg -4.4078186E-09 2.1564645E-08 gauss-seidel spectral radius is 0.9883850 estimated iterations to convergence 76 setup time was (sec) 0.5500000 now iterating at: 23:22:45 rms-change max change #iterations 0.1598119 24.59734 at 10iterations 1.7858876E-02 2.645554 at 20iterations 1.9371281E-03 0.2963276 at 30iterations 2.5782391E-04 4.0425301E-02 at 40iterations 7.1887785E-05 1.3752699E-02 at 50iterations finished qdiffx linear iterations at : 23:22:48 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 7.1887785E-05 1.3752699E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 23:22:49 3.902u 0.273s 0:04.56 91.4% 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 23:22:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 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: 2.005973 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 2.005973 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 334.5995 centred at (gu) : 95.39920 93.19739 90.55711 assigned negative charge : -333.0998 centred at (gu) : 95.24724 92.79238 89.88347 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21136 grid for indexing accessible points = 1.400000 m= 26989 mr = 51359 m= 4527 mr = 19652 m= 345 mr = 2857 m= 8 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 16795 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) : 0.6686575 object centre at (A) : 10.34650 3.073501 16.07550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3170936E-02 -6.5384693E-03 midg,1,midg; midg,igrid,midg 1.5173857E-02 7.7032343E-02 1,midg,midg; igrid,midg,midg -1.5347065E-02 -3.3005924E-04 gauss-seidel spectral radius is 0.9987408 estimated iterations to convergence 223 setup time was (sec) 0.9400000 now iterating at: 23:22:50 rms-change max change #iterations 4.320258 227.2099 at 10iterations 2.084420 77.19611 at 20iterations 1.000313 33.04037 at 30iterations 0.4845547 17.63639 at 40iterations 0.2336763 7.365663 at 50iterations 0.1128571 3.489157 at 60iterations 5.4615360E-02 1.749614 at 70iterations 2.6463894E-02 0.8034172 at 80iterations 1.2779905E-02 0.3865310 at 90iterations 6.1835367E-03 0.2039204 at 100iterations 3.0265502E-03 0.1007867 at 110iterations 1.5092880E-03 4.6618462E-02 at 120iterations finished qdiffx linear iterations at : 23:22:58 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 1.5092880E-03 4.6618462E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.210000 DelPhi exited at 23:22:59 9.215u 0.284s 0:10.08 94.1% 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 Sun Oct 9 2011 at 23:22:59 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 = 2266 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: 3.008959 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 3.008959 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 334.5995 centred at (gu) : 98.09856 94.79593 90.83572 assigned negative charge : -333.0998 centred at (gu) : 97.87090 94.18858 89.82523 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 174337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21136 grid for indexing accessible points = 1.400000 m= 86983 mr = 124255 m= 31746 mr = 70653 m= 8194 mr = 25240 m= 1543 mr = 6164 m= 154 mr = 1135 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 75407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 17016 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) : 2.005973 object centre at (A) : 10.34650 3.073501 16.07550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8048221 -0.1818574 midg,1,midg; midg,igrid,midg 0.2168415 0.7524015 1,midg,midg; igrid,midg,midg -0.2211350 4.4659320E-02 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 1.990000 now iterating at: 23:23:01 rms-change max change #iterations 10.02609 432.4415 at 10iterations 5.917867 134.1746 at 20iterations 3.498272 71.11994 at 30iterations 2.055575 40.98664 at 40iterations 1.206944 24.35321 at 50iterations 0.7063269 14.62707 at 60iterations 0.4128641 7.870751 at 70iterations 0.2409636 4.263782 at 80iterations 0.1402348 2.732866 at 90iterations 8.1793353E-02 1.429230 at 100iterations 4.7716148E-02 0.8946877 at 110iterations 2.7737545E-02 0.4780941 at 120iterations 1.6146867E-02 0.3425827 at 130iterations 9.4181690E-03 0.1613874 at 140iterations 5.4853735E-03 0.1001434 at 150iterations 3.2035096E-03 6.1638832E-02 at 160iterations 1.8765281E-03 3.4580231E-02 at 170iterations 1.1091939E-03 2.1775186E-02 at 180iterations finished qdiffx linear iterations at : 23:23:15 total time elapsed so far: 15.38000 # loops : 180 mean,max change (kT/e) : 1.1091939E-03 2.1775186E-02 energy calculations done at 15.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 23:23:16 15.546u 0.323s 0:16.77 94.5% 0+0k 0+0io 0pf+0w