Sat Oct 15 14:18:52 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 14:18:53 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4759 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5126211 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): -16.68300 37.07600 ymin,ymax (A): -30.93900 33.99500 zmin,zma (A): -3.840000 65.60700 x,y,z range (A): 53.75900 64.93401 69.44701 scale (grids/A): 0.5126211 object centre (A): 10.19650 1.528001 30.88350 number of atom coordinates read : 4759 total number of charged atoms : 4512 net assigned charge : 6.800034 assigned positive charge : 714.1716 centred at (gu) : 89.89692 90.74437 88.38037 assigned negative charge : -707.3761 centred at (gu) : 89.79973 90.81357 88.36437 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8012 nv = 96 ne = 84 npr = 95437 no. pairs analyzed = 95437 no. exposed pairs = 6207 no. arc points = 42935 no. surface atoms = 2068 nbur = 2691 mkacc time = 0.1600000 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= 323 mr = 4125 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4043 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10522 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4927344E-11 1.0080916E-10 midg,1,midg; midg,igrid,midg 2.4644370E-10 -1.0700950E-10 1,midg,midg; igrid,midg,midg -1.7134461E-10 3.6567968E-10 gauss-seidel spectral radius is 0.9805412 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 14:18:53 rms-change max change #iterations 7.0263065E-02 10.51299 at 10iterations 4.2184121E-03 0.6796398 at 20iterations 5.2665418E-04 7.8912735E-02 at 30iterations 1.9555027E-04 3.1533599E-02 at 40iterations 8.4567480E-05 1.5077233E-02 at 50iterations finished qdiffx linear iterations at : 14:18:57 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 8.4567480E-05 1.5077233E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:18:58 4.021u 0.227s 0:05.06 83.7% 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 14:18:58 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4759 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.537863 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): -16.68300 37.07600 ymin,ymax (A): -30.93900 33.99500 zmin,zma (A): -3.840000 65.60700 x,y,z range (A): 53.75900 64.93401 69.44701 scale (grids/A): 1.537863 object centre (A): 10.19650 1.528001 30.88350 number of atom coordinates read : 4759 total number of charged atoms : 4512 net assigned charge : 6.800034 assigned positive charge : 714.1716 centred at (gu) : 89.68920 92.23206 85.14005 assigned negative charge : -707.3761 centred at (gu) : 89.39890 92.44051 85.09305 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26434 mr = 61930 m= 2376 mr = 17405 m= 56 mr = 1068 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.4300000 number of dielectric boundary points 39256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 561 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34025 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) : 0.5126211 object centre at (A) : 10.19650 1.528001 30.88350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5060893E-03 2.0987824E-02 midg,1,midg; midg,igrid,midg 2.2603106E-03 -1.4811470E-02 1,midg,midg; igrid,midg,midg -2.9721874E-04 1.0545657E-02 gauss-seidel spectral radius is 0.9981342 estimated iterations to convergence 184 setup time was (sec) 0.6700000 now iterating at: 14:18:58 rms-change max change #iterations 3.833021 162.1458 at 10iterations 1.578611 51.64968 at 20iterations 0.6520659 21.26885 at 30iterations 0.2693255 8.568932 at 40iterations 0.1111306 3.912519 at 50iterations 4.5944680E-02 1.645437 at 60iterations 1.8990314E-02 0.6324906 at 70iterations 7.8441547E-03 0.2425900 at 80iterations 3.2774869E-03 0.1016474 at 90iterations 1.3770985E-03 4.8456192E-02 at 100iterations 5.9964863E-04 1.9866943E-02 at 110iterations 2.8700341E-04 1.0593414E-02 at 120iterations finished qdiffx linear iterations at : 14:19:08 total time elapsed so far: 8.490000 # loops : 120 mean,max change (kT/e) : 2.8700341E-04 1.0593414E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 14:19:08 8.616u 0.220s 0:10.62 83.1% 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 14:19:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4759 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.306795 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): -16.68300 37.07600 ymin,ymax (A): -30.93900 33.99500 zmin,zma (A): -3.840000 65.60700 x,y,z range (A): 53.75900 64.93401 69.44701 scale (grids/A): 2.306795 object centre (A): 10.19650 1.528001 30.88350 number of atom coordinates read : 4759 total number of charged atoms : 4512 net assigned charge : 6.800034 assigned positive charge : 714.1716 centred at (gu) : 89.53339 93.34783 82.70958 assigned negative charge : -707.3761 centred at (gu) : 89.09822 93.66079 82.63965 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 211503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94697 mr = 152541 m= 23993 mr = 73542 m= 3424 mr = 16949 m= 233 mr = 2097 m= 2 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 1.100000 number of dielectric boundary points 88620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 36004 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) : 1.537863 object centre at (A) : 10.19650 1.528001 30.88350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1307029 0.5072388 midg,1,midg; midg,igrid,midg -7.4633598E-02 -0.3155082 1,midg,midg; igrid,midg,midg -2.3574983E-03 0.1490666 gauss-seidel spectral radius is 0.9991716 estimated iterations to convergence 274 setup time was (sec) 1.360000 now iterating at: 14:19:11 rms-change max change #iterations 10.34041 340.9615 at 10iterations 5.934218 136.6764 at 20iterations 3.389876 85.47612 at 30iterations 1.919719 41.08481 at 40iterations 1.086247 23.76877 at 50iterations 0.6125275 14.45425 at 60iterations 0.3446398 6.900768 at 70iterations 0.1931899 3.896690 at 80iterations 0.1083322 2.072077 at 90iterations 6.0618822E-02 1.204369 at 100iterations 3.3831812E-02 0.6893506 at 110iterations 1.8945619E-02 0.3521576 at 120iterations 1.0568129E-02 0.2247906 at 130iterations 5.9018466E-03 0.1117516 at 140iterations 3.2879838E-03 6.6442490E-02 at 150iterations 1.8327568E-03 3.5034180E-02 at 160iterations 1.0244334E-03 1.8831253E-02 at 170iterations 5.7042745E-04 1.0481834E-02 at 180iterations finished qdiffx linear iterations at : 14:19:29 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 5.7042745E-04 1.0481834E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 14:19:30 13.515u 0.226s 0:21.20 64.7% 0+0k 0+0io 0pf+0w