Sun Oct 9 08:14:38 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 Sun Oct 9 2011 at 08:14:38 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5552003 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 0.5552003 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500029 assigned positive charge : 484.2530 centred at (gu) : 88.42203 91.37389 89.91336 assigned negative charge : -474.7542 centred at (gu) : 88.39645 91.38026 89.96521 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6580 nv = 96 ne = 84 npr = 65709 no. pairs analyzed = 65709 no. exposed pairs = 4143 no. arc points = 29943 no. surface atoms = 1376 nbur = 1889 mkacc time = 0.1400000 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 = 1.540000 m= 280 mr = 3423 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3600000 number of dielectric boundary points 3421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2877 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8398 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3836700E-09 3.2125463E-10 midg,1,midg; midg,igrid,midg 6.5700789E-10 1.0824148E-09 1,midg,midg; igrid,midg,midg 8.5305230E-10 7.5508833E-10 gauss-seidel spectral radius is 0.9832933 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 08:14:39 rms-change max change #iterations 8.1108585E-02 12.14604 at 10iterations 5.7863095E-03 0.8685684 at 20iterations 4.5602021E-04 6.9108963E-02 at 30iterations 5.9321010E-05 8.3408356E-03 at 40iterations 1.1268587E-05 1.6822815E-03 at 50iterations finished qdiffx linear iterations at : 08:14:42 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.1268587E-05 1.6822815E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 08:14:42 3.153u 0.155s 0:03.59 91.9% 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 08:14:42 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.665601 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 1.665601 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500029 assigned positive charge : 484.2530 centred at (gu) : 85.26527 94.12119 89.73943 assigned negative charge : -474.7542 centred at (gu) : 85.18893 94.14051 89.89550 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 23355 mr = 49313 m= 2557 mr = 16386 m= 71 mr = 1363 m= 1 mr = 12 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 0.5200000 number of dielectric boundary points 31706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 23667 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) : 0.5552003 object centre at (A) : 49.81150 34.03650 3.359500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4905153E-03 7.1807685E-03 midg,1,midg; midg,igrid,midg 4.2540375E-03 1.0695253E-02 1,midg,midg; igrid,midg,midg 3.6223520E-02 1.7481901E-02 gauss-seidel spectral radius is 0.9982942 estimated iterations to convergence 192 setup time was (sec) 0.7800000 now iterating at: 08:14:43 rms-change max change #iterations 3.637790 226.3058 at 10iterations 1.556664 78.02563 at 20iterations 0.6621186 29.86844 at 30iterations 0.2838380 10.38564 at 40iterations 0.1215776 4.165077 at 50iterations 5.2137032E-02 1.808571 at 60iterations 2.2325419E-02 0.7432480 at 70iterations 9.5463870E-03 0.3379326 at 80iterations 4.1099857E-03 0.1376038 at 90iterations 1.7701734E-03 6.3594818E-02 at 100iterations 7.6208718E-04 2.5611877E-02 at 110iterations 3.3000589E-04 1.1152267E-02 at 120iterations finished qdiffx linear iterations at : 08:14:49 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 3.3000589E-04 1.1152267E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 08:14:49 7.001u 0.148s 0:07.42 96.2% 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 08:14:50 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 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: 2.498401 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 2.498401 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500029 assigned positive charge : 484.2530 centred at (gu) : 82.89761 96.18153 89.60878 assigned negative charge : -474.7542 centred at (gu) : 82.78339 96.21069 89.84310 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 168978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 79092 mr = 120610 m= 24296 mr = 62928 m= 4176 mr = 18664 m= 313 mr = 2843 m= 4 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 3416 time to turn everything in is 1.190000 number of dielectric boundary points 71663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 24610 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) : 1.665601 object centre at (A) : 49.81150 34.03650 3.359500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3284189E-02 0.1781576 midg,1,midg; midg,igrid,midg 5.7509698E-02 0.2355191 1,midg,midg; igrid,midg,midg 0.6932974 0.2900251 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.470000 now iterating at: 08:14:51 rms-change max change #iterations 9.365461 378.2466 at 10iterations 5.342320 139.5229 at 20iterations 3.028437 72.89095 at 30iterations 1.714398 43.48536 at 40iterations 0.9642634 20.25099 at 50iterations 0.5414718 11.14370 at 60iterations 0.3038839 6.683766 at 70iterations 0.1702560 3.671631 at 80iterations 9.5350847E-02 2.089146 at 90iterations 5.3160600E-02 1.004387 at 100iterations 2.9642336E-02 0.5870705 at 110iterations 1.6573705E-02 0.3214626 at 120iterations 9.2567988E-03 0.1744576 at 130iterations 5.1683835E-03 0.1008162 at 140iterations 2.8761951E-03 5.4988861E-02 at 150iterations 1.6107388E-03 3.3575773E-02 at 160iterations 8.9933246E-04 1.9239426E-02 at 170iterations 5.0376932E-04 9.2196465E-03 at 180iterations finished qdiffx linear iterations at : 08:15:01 total time elapsed so far: 10.81000 # loops : 180 mean,max change (kT/e) : 5.0376932E-04 9.2196465E-03 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 08:15:01 10.990u 0.179s 0:11.47 97.2% 0+0k 0+0io 0pf+0w