Sat Oct 8 11:34:13 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 Sat Oct 8 2011 at 11:34:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5288176 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 0.5288176 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999951 assigned positive charge : 637.9108 centred at (gu) : 87.92537 89.99606 90.72179 assigned negative charge : -642.9135 centred at (gu) : 87.98853 90.12682 90.78761 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6867 nv = 96 ne = 84 npr = 94960 no. pairs analyzed = 94960 no. exposed pairs = 4402 no. arc points = 30332 no. surface atoms = 1521 nbur = 2745 mkacc time = 0.2100000 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 = 1.596000 m= 228 mr = 3852 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.4500000 number of dielectric boundary points 3240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3056 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3395421E-10 -5.8466082E-10 midg,1,midg; midg,igrid,midg 4.7501730E-10 -8.1311602E-10 1,midg,midg; igrid,midg,midg 2.6476568E-10 -2.7995237E-10 gauss-seidel spectral radius is 0.9816464 estimated iterations to convergence 61 setup time was (sec) 0.6700000 now iterating at: 11:34:14 rms-change max change #iterations 7.5447947E-02 12.12364 at 10iterations 4.7903103E-03 0.7121353 at 20iterations 3.3444693E-04 4.3010712E-02 at 30iterations 3.2531116E-05 5.0048828E-03 at 40iterations 4.6771524E-06 6.7138672E-04 at 50iterations finished qdiffx linear iterations at : 11:34:16 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.6771524E-06 6.7138672E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 11:34:17 3.534u 0.168s 0:04.11 89.7% 0+0k 0+0io 6pf+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 11:34:17 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 = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.586453 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 1.586453 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999951 assigned positive charge : 637.9108 centred at (gu) : 83.77470 89.98695 92.16399 assigned negative charge : -642.9135 centred at (gu) : 83.96487 90.38055 92.36218 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21648 mr = 56705 m= 1969 mr = 14808 m= 48 mr = 951 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 3141 time to turn everything in is 0.5800000 number of dielectric boundary points 30076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 31274 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) : 0.5288176 object centre at (A) : 31.95500 12.91600 11.00150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0380850E-03 -1.9963620E-02 midg,1,midg; midg,igrid,midg 3.2364007E-03 -1.1675218E-02 1,midg,midg; igrid,midg,midg 2.9831309E-02 -7.0764855E-03 gauss-seidel spectral radius is 0.9981652 estimated iterations to convergence 185 setup time was (sec) 0.8700000 now iterating at: 11:34:18 rms-change max change #iterations 3.828789 149.2066 at 10iterations 1.582804 57.53090 at 20iterations 0.6609379 20.86070 at 30iterations 0.2750554 9.398956 at 40iterations 0.1142575 3.776484 at 50iterations 4.7778964E-02 1.515306 at 60iterations 1.9835399E-02 0.6194291 at 70iterations 8.2787564E-03 0.2787666 at 80iterations 3.4538077E-03 0.1256441 at 90iterations 1.4459068E-03 4.7290802E-02 at 100iterations 6.0452864E-04 1.9341946E-02 at 110iterations 2.5271345E-04 8.4676743E-03 at 120iterations finished qdiffx linear iterations at : 11:34:25 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 2.5271345E-04 8.4676743E-03 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 11:34:25 7.538u 0.174s 0:08.24 93.4% 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 8 2011 at 11:34:25 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 = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.379679 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 2.379679 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999951 assigned positive charge : 637.9108 centred at (gu) : 80.66178 89.98002 93.24563 assigned negative charge : -642.9135 centred at (gu) : 80.94724 90.57056 93.54317 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 184438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 78549 mr = 138483 m= 19863 mr = 62825 m= 2946 mr = 14731 m= 196 mr = 1969 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.7300001 no. cavity mid-points inaccessible to solvent = 10267 time to turn everything in is 1.340000 number of dielectric boundary points 67904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 32825 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) : 1.586453 object centre at (A) : 31.95500 12.91600 11.00150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2370562 -0.3105412 midg,1,midg; midg,igrid,midg 1.6104363E-02 -0.1617875 1,midg,midg; igrid,midg,midg 0.8866737 -0.4033851 gauss-seidel spectral radius is 0.9991450 estimated iterations to convergence 270 setup time was (sec) 1.640000 now iterating at: 11:34:27 rms-change max change #iterations 9.923906 314.0453 at 10iterations 5.545791 126.7303 at 20iterations 3.101168 62.97417 at 30iterations 1.726151 36.79762 at 40iterations 0.9568989 20.21759 at 50iterations 0.5305067 10.72265 at 60iterations 0.2930568 5.493662 at 70iterations 0.1622961 2.949950 at 80iterations 8.9785010E-02 1.712486 at 90iterations 4.9494199E-02 1.028816 at 100iterations 2.7393589E-02 0.5455456 at 110iterations 1.5121246E-02 0.2909393 at 120iterations 8.3591631E-03 0.1539006 at 130iterations 4.6032034E-03 8.3591461E-02 at 140iterations 2.5435826E-03 4.8500061E-02 at 150iterations 1.4022951E-03 2.4663925E-02 at 160iterations 7.7474106E-04 1.5028000E-02 at 170iterations 4.2841301E-04 7.8830719E-03 at 180iterations finished qdiffx linear iterations at : 11:34:38 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 4.2841301E-04 7.8830719E-03 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 11:34:39 12.556u 0.227s 0:13.31 95.9% 0+0k 0+0io 0pf+0w