Sat Oct 15 13:17:00 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 15 2011 at 13:17:00 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5211764 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 0.5211764 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.740034 assigned positive charge : 831.2908 centred at (gu) : 88.09981 89.28236 88.62959 assigned negative charge : -825.5572 centred at (gu) : 88.01281 89.29268 88.56316 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9428 nv = 96 ne = 84 npr = 109726 no. pairs analyzed = 109726 no. exposed pairs = 6273 no. arc points = 43029 no. surface atoms = 2126 nbur = 3278 mkacc time = 0.2900000 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 = 1.652000 m= 332 mr = 5303 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4307 ## 587 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4573812E-10 3.1393882E-10 midg,1,midg; midg,igrid,midg 2.2737363E-10 7.8560408E-11 1,midg,midg; igrid,midg,midg -4.4567575E-10 3.3138550E-10 gauss-seidel spectral radius is 0.9812078 estimated iterations to convergence 60 setup time was (sec) 0.9200000 now iterating at: 13:17:01 rms-change max change #iterations 8.7716945E-02 13.29711 at 10iterations 1.0172568E-02 1.579079 at 20iterations 3.8045151E-03 0.6107597 at 30iterations 1.6389438E-03 0.2679596 at 40iterations 7.1125472E-04 0.1165619 at 50iterations finished qdiffx linear iterations at : 13:17:06 total time elapsed so far: 5.430000 # loops : 50 mean,max change (kT/e) : 7.1125472E-04 0.1165619 energy calculations done at 5.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.590000 DelPhi exited at 13:17:06 5.594u 0.462s 0:06.34 95.4% 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 15 2011 at 13:17:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.563529 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 1.563529 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.740034 assigned positive charge : 831.2908 centred at (gu) : 84.29793 87.84570 85.88745 assigned negative charge : -825.5572 centred at (gu) : 84.03800 87.87785 85.68943 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 106943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 33893 mr = 77253 m= 3202 mr = 23795 m= 75 mr = 1520 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 41538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 6 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 39673 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) : 0.5211764 object centre at (A) : 36.10950 22.17900 32.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5902573E-02 2.4075067E-02 midg,1,midg; midg,igrid,midg 1.8586952E-02 5.2739666E-03 1,midg,midg; igrid,midg,midg -9.2269350E-03 4.1693216E-03 gauss-seidel spectral radius is 0.9982370 estimated iterations to convergence 189 setup time was (sec) 1.330000 now iterating at: 13:17:08 rms-change max change #iterations 4.340885 162.9897 at 10iterations 1.832879 58.05014 at 20iterations 0.7765405 22.07110 at 30iterations 0.3293993 9.461441 at 40iterations 0.1409201 4.015480 at 50iterations 6.1053127E-02 1.931705 at 60iterations 2.7589869E-02 0.8341980 at 70iterations 1.3670158E-02 0.4562378 at 80iterations 7.9065757E-03 0.2856522 at 90iterations 5.1859585E-03 0.1733246 at 100iterations 3.6850453E-03 0.1195755 at 110iterations 2.7019733E-03 8.7528229E-02 at 120iterations finished qdiffx linear iterations at : 13:17:20 total time elapsed so far: 13.16000 # loops : 120 mean,max change (kT/e) : 2.7019733E-03 8.7528229E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 13:17:20 13.332u 0.517s 0:14.25 97.1% 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 Sat Oct 15 2011 at 13:17:21 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.345294 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 2.345294 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.740034 assigned positive charge : 831.2908 centred at (gu) : 81.44666 86.76799 83.83063 assigned negative charge : -825.5572 centred at (gu) : 81.05693 86.81677 83.53413 start vw surface at 0.1900000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 249258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 119356 mr = 188597 m= 32900 mr = 96326 m= 4756 mr = 24731 m= 290 mr = 3046 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 93733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 41869 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) : 1.563529 object centre at (A) : 36.10950 22.17900 32.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3555142 0.6757137 midg,1,midg; midg,igrid,midg 0.2946763 3.9487489E-02 1,midg,midg; igrid,midg,midg -0.3322283 7.3180094E-02 gauss-seidel spectral radius is 0.9991998 estimated iterations to convergence 279 setup time was (sec) 2.670000 now iterating at: 13:17:24 rms-change max change #iterations 11.38787 289.2737 at 10iterations 6.579567 148.3267 at 20iterations 3.771146 76.27161 at 30iterations 2.147135 39.23768 at 40iterations 1.221035 23.53329 at 50iterations 0.6937965 11.69643 at 60iterations 0.3924701 7.346951 at 70iterations 0.2222530 3.664627 at 80iterations 0.1254989 2.110618 at 90iterations 7.1317673E-02 1.239746 at 100iterations 4.0666517E-02 0.6914885 at 110iterations 2.3506889E-02 0.4123132 at 120iterations 1.3959027E-02 0.2520523 at 130iterations 8.6433245E-03 0.1721992 at 140iterations 5.6769736E-03 0.1253796 at 150iterations 4.0129935E-03 8.4938049E-02 at 160iterations 3.0296752E-03 6.2480927E-02 at 170iterations 2.3831783E-03 4.8233032E-02 at 180iterations finished qdiffx linear iterations at : 13:17:45 total time elapsed so far: 24.27000 # loops : 180 mean,max change (kT/e) : 2.3831783E-03 4.8233032E-02 energy calculations done at 24.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.44000 DelPhi exited at 13:17:46 24.445u 0.576s 0:25.32 98.7% 0+0k 0+0io 0pf+0w