Sun Oct 9 14:43:52 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 Sun Oct 9 2011 at 14:43:52 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 has a net charge of -2.0000 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: 0.5641838 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 0.5641838 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500014 assigned positive charge : 453.4221 centred at (gu) : 89.96043 89.91155 88.79336 assigned negative charge : -449.9233 centred at (gu) : 89.93840 90.11505 88.90627 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6410 nv = 96 ne = 84 npr = 57958 no. pairs analyzed = 57958 no. exposed pairs = 4041 no. arc points = 29776 no. surface atoms = 1340 nbur = 1659 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 = 1.512000 m= 285 mr = 3020 m= 1 mr = 11 m= 0 mr = 0 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 3665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3026 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4979439E-09 -7.9476764E-10 midg,1,midg; midg,igrid,midg 3.0593215E-09 -2.2453042E-09 1,midg,midg; igrid,midg,midg 1.2966622E-10 6.9432499E-10 gauss-seidel spectral radius is 0.9838095 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 14:43:53 rms-change max change #iterations 8.1393175E-02 14.33822 at 10iterations 6.0340301E-03 0.9615803 at 20iterations 4.3490995E-04 7.3001862E-02 at 30iterations 3.2446980E-05 5.4473877E-03 at 40iterations 2.6376811E-06 4.1580200E-04 at 50iterations finished qdiffx linear iterations at : 14:43:56 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.6376811E-06 4.1580200E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 14:43:56 3.460u 0.185s 0:03.96 91.9% 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 Sun Oct 9 2011 at 14:43:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 has a net charge of -2.0000 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: 1.692551 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 1.692551 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500014 assigned positive charge : 453.4221 centred at (gu) : 89.88055 89.73418 86.37915 assigned negative charge : -449.9233 centred at (gu) : 89.81499 90.34486 86.71857 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29776 grid for indexing accessible points = 1.400000 m= 20225 mr = 44810 m= 2212 mr = 12943 m= 76 mr = 982 m= 0 mr = 13 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.3400000 number of dielectric boundary points 33833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 22053 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) : 0.5641838 object centre at (A) : -0.1989994 5.312002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2184906E-02 -5.8928081E-03 midg,1,midg; midg,igrid,midg 1.9400384E-02 -1.5201949E-02 1,midg,midg; igrid,midg,midg 1.3022006E-03 -1.3988767E-02 gauss-seidel spectral radius is 0.9983334 estimated iterations to convergence 194 setup time was (sec) 0.5600000 now iterating at: 14:43:57 rms-change max change #iterations 3.620478 154.8834 at 10iterations 1.556136 62.82999 at 20iterations 0.6722699 25.69492 at 30iterations 0.2888689 10.19764 at 40iterations 0.1247209 4.522271 at 50iterations 5.3800561E-02 2.049995 at 60iterations 2.3134094E-02 0.8102989 at 70iterations 1.0019631E-02 0.3293915 at 80iterations 4.3087252E-03 0.1430912 at 90iterations 1.8601711E-03 6.5265656E-02 at 100iterations 8.0428348E-04 2.7881622E-02 at 110iterations 3.4688142E-04 1.1259079E-02 at 120iterations finished qdiffx linear iterations at : 14:44:04 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 3.4688142E-04 1.1259079E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 14:44:05 7.915u 0.201s 0:08.39 96.6% 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 Sun Oct 9 2011 at 14:44:05 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 has a net charge of -2.0000 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: 2.538827 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 2.538827 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500014 assigned positive charge : 453.4221 centred at (gu) : 89.82059 89.60096 84.56850 assigned negative charge : -449.9233 centred at (gu) : 89.72240 90.51718 85.07771 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 162419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29776 grid for indexing accessible points = 1.400000 m= 70485 mr = 110115 m= 19492 mr = 53740 m= 3280 mr = 13555 m= 281 mr = 1993 m= 9 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.8300000 number of dielectric boundary points 76438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22834 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) : 1.692551 object centre at (A) : -0.1989994 5.312002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5513397 -0.1334814 midg,1,midg; midg,igrid,midg 0.1789808 -0.1589500 1,midg,midg; igrid,midg,midg 5.3912669E-02 -0.2411294 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.070000 now iterating at: 14:44:06 rms-change max change #iterations 9.372518 380.6468 at 10iterations 5.389451 148.0698 at 20iterations 3.080253 76.20675 at 30iterations 1.750680 43.36044 at 40iterations 0.9947764 22.87382 at 50iterations 0.5629669 12.46178 at 60iterations 0.3178688 8.190467 at 70iterations 0.1789692 3.903740 at 80iterations 0.1009726 2.309165 at 90iterations 5.6682292E-02 1.239586 at 100iterations 3.1925313E-02 0.6544313 at 110iterations 1.7910901E-02 0.4043760 at 120iterations 1.0035204E-02 0.1917804 at 130iterations 5.6470060E-03 0.1315117 at 140iterations 3.1636015E-03 6.6810131E-02 at 150iterations 1.7742468E-03 3.6244392E-02 at 160iterations 9.9614402E-04 2.0655632E-02 at 170iterations 5.6035805E-04 1.1833191E-02 at 180iterations finished qdiffx linear iterations at : 14:44:17 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 5.6035805E-04 1.1833191E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 14:44:18 12.672u 0.217s 0:13.15 97.9% 0+0k 0+0io 0pf+0w