Sat Oct 15 14:36:53 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 14:36:54 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 = 2989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5389529 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): -2.219000 63.83500 ymin,ymax (A): 13.65300 60.91800 zmin,zma (A): -9.430000 36.97700 x,y,z range (A): 66.05400 47.26500 46.40700 scale (grids/A): 0.5389529 object centre (A): 30.80800 37.28550 13.77350 number of atom coordinates read : 2989 total number of charged atoms : 2848 net assigned charge : -0.9999841 assigned positive charge : 446.1250 centred at (gu) : 89.12834 90.34592 89.78190 assigned negative charge : -447.1262 centred at (gu) : 89.09444 90.48038 89.66901 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 59960 no. pairs analyzed = 59960 no. exposed pairs = 3974 no. arc points = 28026 no. surface atoms = 1338 nbur = 1651 mkacc time = 0.1000000 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= 218 mr = 2679 m= 0 mr = 5 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2842 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7375 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6243189E-10 5.0046389E-10 midg,1,midg; midg,igrid,midg 5.8247945E-10 -8.0893775E-10 1,midg,midg; igrid,midg,midg -2.6788632E-10 1.0573011E-10 gauss-seidel spectral radius is 0.9822598 estimated iterations to convergence 62 setup time was (sec) 0.4400000 now iterating at: 14:36:54 rms-change max change #iterations 6.5601699E-02 12.69830 at 10iterations 4.1344995E-03 0.7157536 at 20iterations 2.6534649E-04 4.1246414E-02 at 30iterations 1.7028970E-05 2.8800964E-03 at 40iterations 1.1290348E-06 1.8310547E-04 at 50iterations finished qdiffx linear iterations at : 14:36:59 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.1290348E-06 1.8310547E-04 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 14:37:00 3.522u 0.255s 0:06.33 59.5% 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 14:37:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.616859 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): -2.219000 63.83500 ymin,ymax (A): 13.65300 60.91800 zmin,zma (A): -9.430000 36.97700 x,y,z range (A): 66.05400 47.26500 46.40700 scale (grids/A): 1.616859 object centre (A): 30.80800 37.28550 13.77350 number of atom coordinates read : 2989 total number of charged atoms : 2848 net assigned charge : -0.9999841 assigned positive charge : 446.1250 centred at (gu) : 87.38422 91.03721 89.34499 assigned negative charge : -447.1262 centred at (gu) : 87.28282 91.44072 89.00665 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28026 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 17593 mr = 40137 m= 1611 mr = 11381 m= 46 mr = 686 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 958 time to turn everything in is 0.3000000 number of dielectric boundary points 28627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 21726 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) : 0.5389529 object centre at (A) : 30.80800 37.28550 13.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5482910E-03 4.3704007E-03 midg,1,midg; midg,igrid,midg 5.2835410E-03 -1.5087139E-02 1,midg,midg; igrid,midg,midg -1.3353303E-02 -5.0939610E-03 gauss-seidel spectral radius is 0.9981490 estimated iterations to convergence 185 setup time was (sec) 0.5200000 now iterating at: 14:37:01 rms-change max change #iterations 3.234861 136.1254 at 10iterations 1.325797 53.44320 at 20iterations 0.5487359 23.18139 at 30iterations 0.2262738 8.536182 at 40iterations 9.3560398E-02 3.573898 at 50iterations 3.8539108E-02 1.722357 at 60iterations 1.5854502E-02 0.5821571 at 70iterations 6.5541286E-03 0.2606220 at 80iterations 2.7076937E-03 0.1145706 at 90iterations 1.1190331E-03 4.0384293E-02 at 100iterations 4.6107959E-04 1.7541885E-02 at 110iterations 1.9095808E-04 6.9896579E-03 at 120iterations finished qdiffx linear iterations at : 14:37:14 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 1.9095808E-04 6.9896579E-03 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 14:37:15 8.045u 0.214s 0:14.94 55.2% 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 Sat Oct 15 2011 at 14:37:15 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 = 2989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.425288 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): -2.219000 63.83500 ymin,ymax (A): 13.65300 60.91800 zmin,zma (A): -9.430000 36.97700 x,y,z range (A): 66.05400 47.26500 46.40700 scale (grids/A): 2.425288 object centre (A): 30.80800 37.28550 13.77350 number of atom coordinates read : 2989 total number of charged atoms : 2848 net assigned charge : -0.9999841 assigned positive charge : 446.1250 centred at (gu) : 86.07632 91.55551 89.01710 assigned negative charge : -447.1262 centred at (gu) : 85.92420 92.16096 88.50994 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 143206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28026 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61694 mr = 98930 m= 16531 mr = 47066 m= 2333 mr = 11890 m= 123 mr = 1334 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 3232 time to turn everything in is 0.7400000 number of dielectric boundary points 64629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22756 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) : 1.616859 object centre at (A) : 30.80800 37.28550 13.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7725342E-02 5.7250477E-02 midg,1,midg; midg,igrid,midg 9.2397459E-02 -0.2275343 1,midg,midg; igrid,midg,midg -0.5646096 6.0375676E-02 gauss-seidel spectral radius is 0.9991292 estimated iterations to convergence 268 setup time was (sec) 1.000000 now iterating at: 14:37:18 rms-change max change #iterations 8.502542 290.8383 at 10iterations 4.734825 127.2567 at 20iterations 2.622628 67.14377 at 30iterations 1.450371 36.01030 at 40iterations 0.7962358 19.24812 at 50iterations 0.4383031 10.42879 at 60iterations 0.2402627 5.352365 at 70iterations 0.1318952 2.960418 at 80iterations 7.2192244E-02 1.541328 at 90iterations 3.9503947E-02 0.7989721 at 100iterations 2.1626767E-02 0.4682956 at 110iterations 1.1842771E-02 0.2670841 at 120iterations 6.4664874E-03 0.1429615 at 130iterations 3.5386488E-03 7.8034639E-02 at 140iterations 1.9328832E-03 4.2758942E-02 at 150iterations 1.0575021E-03 2.2552490E-02 at 160iterations 5.7968590E-04 1.2252808E-02 at 170iterations 3.1663562E-04 6.3493252E-03 at 180iterations finished qdiffx linear iterations at : 14:37:42 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 3.1663562E-04 6.3493252E-03 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 14:37:43 13.075u 0.259s 0:27.66 48.1% 0+0k 0+0io 0pf+0w