Mon Oct 10 13:59:15 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 Mon Oct 10 2011 at 13:59:15 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 = 4389 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: 0.5084116 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 0.5084116 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.499949 assigned positive charge : 659.4897 centred at (gu) : 88.66513 89.96698 91.78352 assigned negative charge : -662.9922 centred at (gu) : 88.68024 90.08944 91.83429 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7130 nv = 96 ne = 84 npr = 91544 no. pairs analyzed = 91544 no. exposed pairs = 5095 no. arc points = 34109 no. surface atoms = 1741 nbur = 2648 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 = 1.680000 m= 258 mr = 3965 m= 1 mr = 10 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 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3520 ## 551 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1069530E-11 -2.4897576E-10 midg,1,midg; midg,igrid,midg 2.2140333E-10 -3.1133979E-10 1,midg,midg; igrid,midg,midg -1.3512536E-11 -5.3675144E-11 gauss-seidel spectral radius is 0.9801801 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 13:59:16 rms-change max change #iterations 6.3333720E-02 12.07886 at 10iterations 4.1004168E-03 0.6510868 at 20iterations 7.1249931E-04 9.8812103E-02 at 30iterations 2.2650784E-04 3.4114838E-02 at 40iterations 7.7031313E-05 1.2023926E-02 at 50iterations finished qdiffx linear iterations at : 13:59:19 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 7.7031313E-05 1.2023926E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:59:19 3.628u 0.193s 0:04.36 87.3% 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 Mon Oct 10 2011 at 13:59:19 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 = 4389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.525235 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 1.525235 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.499949 assigned positive charge : 659.4897 centred at (gu) : 85.99438 89.89996 95.34920 assigned negative charge : -662.9922 centred at (gu) : 86.04000 90.26781 95.50256 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 81302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24441 mr = 58169 m= 2119 mr = 16973 m= 36 mr = 936 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.4100000 number of dielectric boundary points 31819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 31887 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) : 0.5084116 object centre at (A) : 30.55750 13.21300 10.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8630103E-03 -1.3105653E-02 midg,1,midg; midg,igrid,midg 3.3322852E-03 -1.0269101E-02 1,midg,midg; igrid,midg,midg 6.5207710E-03 1.2022480E-02 gauss-seidel spectral radius is 0.9980365 estimated iterations to convergence 179 setup time was (sec) 0.6700000 now iterating at: 13:59:20 rms-change max change #iterations 3.555669 143.3629 at 10iterations 1.427864 49.00761 at 20iterations 0.5760514 20.10353 at 30iterations 0.2327095 7.467834 at 40iterations 9.4092458E-02 2.943071 at 50iterations 3.8168352E-02 1.367263 at 60iterations 1.5487345E-02 0.5958304 at 70iterations 6.3652890E-03 0.2128544 at 80iterations 2.6842451E-03 8.9767456E-02 at 90iterations 1.1964174E-03 4.1437149E-02 at 100iterations 5.9026037E-04 2.2026062E-02 at 110iterations 3.2868003E-04 1.1230469E-02 at 120iterations finished qdiffx linear iterations at : 13:59:28 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 3.2868003E-04 1.1230469E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 13:59:29 8.643u 0.258s 0:10.01 88.8% 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 Mon Oct 10 2011 at 13:59:29 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 = 4389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.287852 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 2.287852 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.499949 assigned positive charge : 659.4897 centred at (gu) : 83.99141 89.84949 98.02357 assigned negative charge : -662.9922 centred at (gu) : 84.05987 90.40160 98.25365 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 189892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87869 mr = 142549 m= 22812 mr = 70548 m= 3124 mr = 16953 m= 134 mr = 1969 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.9800000 number of dielectric boundary points 71785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 33767 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) : 1.525235 object centre at (A) : 30.55750 13.21300 10.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1758881 -0.3115567 midg,1,midg; midg,igrid,midg 3.1790607E-02 -0.1683492 1,midg,midg; igrid,midg,midg 0.2168458 0.2981711 gauss-seidel spectral radius is 0.9991177 estimated iterations to convergence 266 setup time was (sec) 1.220000 now iterating at: 13:59:31 rms-change max change #iterations 9.624710 259.9782 at 10iterations 5.400456 119.9044 at 20iterations 3.006415 63.17983 at 30iterations 1.665845 39.32042 at 40iterations 0.9193751 17.75125 at 50iterations 0.5069617 10.16348 at 60iterations 0.2783161 5.462879 at 70iterations 0.1530708 2.889849 at 80iterations 8.3806798E-02 1.542239 at 90iterations 4.5913093E-02 0.9351425 at 100iterations 2.5162850E-02 0.4908483 at 110iterations 1.3793950E-02 0.2684665 at 120iterations 7.5961202E-03 0.1600494 at 130iterations 4.2173169E-03 8.2697272E-02 at 140iterations 2.3585588E-03 4.6658039E-02 at 150iterations 1.3490400E-03 2.6171684E-02 at 160iterations 7.9785089E-04 1.8470764E-02 at 170iterations 4.9664365E-04 1.0947227E-02 at 180iterations finished qdiffx linear iterations at : 13:59:42 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 4.9664365E-04 1.0947227E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 13:59:43 12.894u 0.247s 0:13.52 97.1% 0+0k 0+0io 0pf+0w