Wed Feb 15 08:55:30 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:30 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 = 3332 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: 0.5384068 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 0.5384068 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 498.9332 centred at (gu) : 90.08627 89.99965 89.90612 assigned negative charge : -509.4345 centred at (gu) : 90.06859 89.81682 90.03444 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6291 nv = 96 ne = 84 npr = 66633 no. pairs analyzed = 66633 no. exposed pairs = 4492 no. arc points = 31289 no. surface atoms = 1483 nbur = 1849 mkacc time = 0.1500000 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= 260 mr = 3165 m= 0 mr = 17 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3700000 number of dielectric boundary points 3369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3149 ## 449 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4461735E-10 -1.2013495E-09 midg,1,midg; midg,igrid,midg -1.5545213E-09 5.3795396E-10 1,midg,midg; igrid,midg,midg -5.7289756E-10 -3.9093631E-10 gauss-seidel spectral radius is 0.9822510 estimated iterations to convergence 62 setup time was (sec) 0.6000000 now iterating at: 08:55:31 rms-change max change #iterations 7.1495630E-02 10.74944 at 10iterations 4.9076034E-03 0.7925043 at 20iterations 5.3368497E-04 0.1377106 at 30iterations 1.2674034E-04 3.7281036E-02 at 40iterations 3.4976089E-05 1.0442734E-02 at 50iterations finished qdiffx linear iterations at : 08:55:34 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 3.4976089E-05 1.0442734E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 08:55:34 3.543u 0.188s 0:04.28 86.9% 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 Wed Feb 15 2012 at 08:55:35 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 = 3332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.615221 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 1.615221 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 498.9332 centred at (gu) : 90.25798 89.99757 89.71700 assigned negative charge : -509.4345 centred at (gu) : 90.20530 89.44978 90.10262 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21058 mr = 46583 m= 2112 mr = 14171 m= 56 mr = 1089 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3261 time to turn everything in is 0.5400000 number of dielectric boundary points 31237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 24347 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) : 0.5384068 object centre at (A) : 52.70050 107.2345 28.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7328436E-04 -1.0720650E-02 midg,1,midg; midg,igrid,midg -2.4920236E-02 4.8455808E-04 1,midg,midg; igrid,midg,midg -1.0455234E-02 -5.5119568E-03 gauss-seidel spectral radius is 0.9981866 estimated iterations to convergence 187 setup time was (sec) 0.8300000 now iterating at: 08:55:35 rms-change max change #iterations 3.468054 158.4350 at 10iterations 1.431031 57.18493 at 20iterations 0.5972472 21.98318 at 30iterations 0.2485239 8.794744 at 40iterations 0.1036004 3.802212 at 50iterations 4.3167751E-02 1.462830 at 60iterations 1.8092845E-02 0.6421986 at 70iterations 7.5540598E-03 0.2516327 at 80iterations 3.1618152E-03 0.1109247 at 90iterations 1.3476667E-03 5.0223351E-02 at 100iterations 5.8879430E-04 2.2822380E-02 at 110iterations 2.6654333E-04 1.2168884E-02 at 120iterations finished qdiffx linear iterations at : 08:55:42 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.6654333E-04 1.2168884E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 08:55:43 7.601u 0.159s 0:08.46 91.6% 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 Wed Feb 15 2012 at 08:55:43 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 = 3332 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: 2.422831 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): 19.64000 85.76100 ymin,ymax (A): 80.27600 134.1930 zmin,zma (A): 3.866000 52.91300 x,y,z range (A): 66.12100 53.91699 49.04700 scale (grids/A): 2.422831 object centre (A): 52.70050 107.2345 28.38950 number of atom coordinates read : 3332 total number of charged atoms : 3185 net assigned charge : -10.49998 assigned positive charge : 498.9332 centred at (gu) : 90.38674 89.99623 89.57552 assigned negative charge : -509.4345 centred at (gu) : 90.30782 89.17454 90.15401 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73006 mr = 114571 m= 20501 mr = 56709 m= 3401 mr = 15276 m= 244 mr = 2287 m= 1 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 11132 time to turn everything in is 1.240000 number of dielectric boundary points 70548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 25435 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) : 1.615221 object centre at (A) : 52.70050 107.2345 28.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1173032E-02 -0.1438201 midg,1,midg; midg,igrid,midg -0.3619105 1.3073239E-02 1,midg,midg; igrid,midg,midg -0.1417876 -1.8588297E-02 gauss-seidel spectral radius is 0.9991506 estimated iterations to convergence 271 setup time was (sec) 1.550000 now iterating at: 08:55:45 rms-change max change #iterations 9.098157 315.6318 at 10iterations 5.118328 153.2117 at 20iterations 2.869457 62.36276 at 30iterations 1.600046 34.41100 at 40iterations 0.8887037 19.37931 at 50iterations 0.4930456 10.16110 at 60iterations 0.2727930 5.807407 at 70iterations 0.1513477 3.080675 at 80iterations 8.3607592E-02 1.989556 at 90iterations 4.6230692E-02 0.9110508 at 100iterations 2.5492951E-02 0.4988136 at 110iterations 1.4095755E-02 0.2889519 at 120iterations 7.7872360E-03 0.1658554 at 130iterations 4.3021790E-03 8.9109421E-02 at 140iterations 2.3898175E-03 4.7291875E-02 at 150iterations 1.3306569E-03 2.8579712E-02 at 160iterations 7.4452511E-04 1.7517090E-02 at 170iterations 4.2333864E-04 1.1045456E-02 at 180iterations finished qdiffx linear iterations at : 08:55:56 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 4.2333864E-04 1.1045456E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 08:55:57 12.972u 0.219s 0:13.91 94.7% 0+0k 0+0io 0pf+0w