Sun Oct 9 18:34:05 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 18:34:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5469434 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 0.5469434 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6210541 assigned positive charge : 787.6975 centred at (gu) : 87.95007 89.26749 89.66417 assigned negative charge : -787.0827 centred at (gu) : 87.85271 89.31323 89.65632 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10097 nv = 96 ne = 84 npr = 103143 no. pairs analyzed = 103143 no. exposed pairs = 6002 no. arc points = 41017 no. surface atoms = 2051 nbur = 3084 mkacc time = 0.2700000 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 = 1.568000 m= 463 mr = 5801 m= 1 mr = 31 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 0.5500000 number of dielectric boundary points 4729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4171 ## 473 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4941584E-11 1.4570628E-10 midg,1,midg; midg,igrid,midg 7.3890905E-10 -4.1114770E-10 1,midg,midg; igrid,midg,midg -1.9087618E-09 7.3944123E-10 gauss-seidel spectral radius is 0.9829218 estimated iterations to convergence 63 setup time was (sec) 0.8500000 now iterating at: 18:34:07 rms-change max change #iterations 0.1025095 11.82102 at 10iterations 9.7216256E-03 1.445915 at 20iterations 2.9613173E-03 0.3414993 at 30iterations 1.3318664E-03 0.1550540 at 40iterations 6.2157807E-04 7.7153854E-02 at 50iterations finished qdiffx linear iterations at : 18:34:12 total time elapsed so far: 5.900000 # loops : 50 mean,max change (kT/e) : 6.2157807E-04 7.7153854E-02 energy calculations done at 5.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.080000 DelPhi exited at 18:34:12 6.088u 0.464s 0:06.94 94.2% 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 Sun Oct 9 2011 at 18:34:12 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.640830 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 1.640830 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6210541 assigned positive charge : 787.6975 centred at (gu) : 83.84869 87.80041 88.99115 assigned negative charge : -787.0827 centred at (gu) : 83.55804 87.93967 88.96912 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 112826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41017 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39055 mr = 81889 m= 4604 mr = 28196 m= 134 mr = 2433 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 44088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 38236 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) : 0.5469434 object centre at (A) : 35.76050 22.27250 29.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3552631E-02 -1.5130745E-02 midg,1,midg; midg,igrid,midg 2.0333659E-02 6.8031889E-03 1,midg,midg; igrid,midg,midg -1.6469689E-02 1.1785719E-02 gauss-seidel spectral radius is 0.9984028 estimated iterations to convergence 199 setup time was (sec) 1.340000 now iterating at: 18:34:14 rms-change max change #iterations 4.747251 160.9104 at 10iterations 2.090750 61.27562 at 20iterations 0.9216519 27.86645 at 30iterations 0.4068456 11.46428 at 40iterations 0.1795232 5.068968 at 50iterations 7.9775251E-02 2.394638 at 60iterations 3.5683934E-02 0.9486430 at 70iterations 1.6371179E-02 0.5160789 at 80iterations 8.0421744E-03 0.2417269 at 90iterations 4.4233603E-03 0.1170769 at 100iterations 2.8019552E-03 7.6585770E-02 at 110iterations 1.9758062E-03 4.8080444E-02 at 120iterations finished qdiffx linear iterations at : 18:34:27 total time elapsed so far: 14.22000 # loops : 120 mean,max change (kT/e) : 1.9758062E-03 4.8080444E-02 energy calculations done at 14.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 18:34:27 14.393u 0.533s 0:15.28 97.6% 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 18:34:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.461246 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 2.461246 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6210541 assigned positive charge : 787.6975 centred at (gu) : 80.77263 86.70036 88.48642 assigned negative charge : -787.0827 centred at (gu) : 80.33713 86.90941 88.45352 start vw surface at 0.1800000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 262348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41017 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 132487 mr = 199184 m= 41498 mr = 108222 m= 7467 mr = 32193 m= 633 mr = 5080 m= 12 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.700000 number of dielectric boundary points 99453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.890000 number of grid points assigned charge 39901 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) : 1.640830 object centre at (A) : 35.76050 22.27250 29.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2704021 -0.3102605 midg,1,midg; midg,igrid,midg 0.1367202 -5.2533865E-02 1,midg,midg; igrid,midg,midg -0.3561975 0.2184565 gauss-seidel spectral radius is 0.9992469 estimated iterations to convergence 288 setup time was (sec) 3.130000 now iterating at: 18:34:31 rms-change max change #iterations 12.04192 279.1948 at 10iterations 7.111550 147.6056 at 20iterations 4.163690 81.82425 at 30iterations 2.421636 43.94511 at 40iterations 1.404222 28.97724 at 50iterations 0.8152757 14.95173 at 60iterations 0.4701081 9.383972 at 70iterations 0.2710446 4.997602 at 80iterations 0.1561461 2.800419 at 90iterations 9.0122432E-02 1.467857 at 100iterations 5.2031085E-02 0.8160896 at 110iterations 3.0273424E-02 0.5265694 at 120iterations 1.7830059E-02 0.2911987 at 130iterations 1.0799644E-02 0.2035522 at 140iterations 6.8143765E-03 0.1187897 at 150iterations 4.6001314E-03 7.9800606E-02 at 160iterations 3.3325746E-03 5.8942318E-02 at 170iterations 2.5747579E-03 4.2820454E-02 at 180iterations finished qdiffx linear iterations at : 18:34:52 total time elapsed so far: 24.39000 # loops : 180 mean,max change (kT/e) : 2.5747579E-03 4.2820454E-02 energy calculations done at 24.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.57000 DelPhi exited at 18:34:53 24.574u 0.550s 0:25.42 98.8% 0+0k 0+0io 0pf+0w