Mon Oct 10 11:46:44 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+sph2.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 = amb2.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 11:46:44 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7283292 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): -20.87800 24.17600 ymin,ymax (A): -7.961000 38.29000 zmin,zma (A): -3.541000 45.33800 x,y,z range (A): 45.05400 46.25100 48.87900 scale (grids/A): 0.7283292 object centre (A): 1.648999 15.16450 20.89850 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 317.2519 centred at (gu) : 88.98814 89.73992 89.86023 assigned negative charge : -323.2520 centred at (gu) : 89.01337 89.82688 90.04010 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7741 nv = 96 ne = 84 npr = 43480 no. pairs analyzed = 43480 no. exposed pairs = 2731 no. arc points = 19234 no. surface atoms = 927 nbur = 1188 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 553 mr = 4263 m= 3 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.2700000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1566 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1897019E-08 -2.2360216E-07 midg,1,midg; midg,igrid,midg -1.3195984E-08 -1.4555039E-07 1,midg,midg; igrid,midg,midg -7.4346048E-08 -8.5157190E-08 gauss-seidel spectral radius is 0.9901802 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 11:46:45 rms-change max change #iterations 0.2339968 29.69631 at 10iterations 3.0642271E-02 3.715794 at 20iterations 3.8989512E-03 0.5567787 at 30iterations 5.0871313E-04 7.9219460E-02 at 40iterations 6.7969049E-05 8.9340210E-03 at 50iterations finished qdiffx linear iterations at : 11:46:48 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 6.7969049E-05 8.9340210E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 11:46:49 4.373u 0.392s 0:05.05 94.2% 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 Mon Oct 10 2011 at 11:46:49 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.184988 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): -20.87800 24.17600 ymin,ymax (A): -7.961000 38.29000 zmin,zma (A): -3.541000 45.33800 x,y,z range (A): 45.05400 46.25100 48.87900 scale (grids/A): 2.184988 object centre (A): 1.648999 15.16450 20.89850 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 317.2519 centred at (gu) : 86.96443 89.21973 89.58067 assigned negative charge : -323.2520 centred at (gu) : 87.04020 89.48051 90.12031 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19234 grid for indexing accessible points = 1.400000 m= 31859 mr = 55106 m= 6870 mr = 23955 m= 710 mr = 4790 m= 19 mr = 386 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1779 time to turn everything in is 0.6800000 number of dielectric boundary points 35846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15743 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) : 0.7283292 object centre at (A) : 1.648999 15.16450 20.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5974358E-03 -0.1252674 midg,1,midg; midg,igrid,midg -2.5955051E-02 -2.9704202E-02 1,midg,midg; igrid,midg,midg -1.7878395E-02 -1.0625697E-03 gauss-seidel spectral radius is 0.9988980 estimated iterations to convergence 238 setup time was (sec) 0.9700000 now iterating at: 11:46:50 rms-change max change #iterations 4.946493 205.4362 at 10iterations 2.489090 80.95090 at 20iterations 1.253979 35.76529 at 30iterations 0.6321403 17.70588 at 40iterations 0.3195721 9.251906 at 50iterations 0.1615200 4.538082 at 60iterations 8.1547804E-02 2.439539 at 70iterations 4.1189492E-02 1.238272 at 80iterations 2.0824870E-02 0.6072720 at 90iterations 1.0526807E-02 0.2929967 at 100iterations 5.3038415E-03 0.1487503 at 110iterations 2.6790013E-03 7.6021194E-02 at 120iterations finished qdiffx linear iterations at : 11:47:00 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 2.6790013E-03 7.6021194E-02 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 11:47:00 10.635u 0.447s 0:11.44 96.7% 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 Mon Oct 10 2011 at 11:47:00 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 3.277481 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): -20.87800 24.17600 ymin,ymax (A): -7.961000 38.29000 zmin,zma (A): -3.541000 45.33800 x,y,z range (A): 45.05400 46.25100 48.87900 scale (grids/A): 3.277481 object centre (A): 1.648999 15.16450 20.89850 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 317.2519 centred at (gu) : 85.44672 88.82963 89.37100 assigned negative charge : -323.2520 centred at (gu) : 85.56033 89.22080 90.18054 start vw surface at 0.1000000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 185724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19234 grid for indexing accessible points = 1.400000 m= 97762 mr = 132907 m= 41602 mr = 80532 m= 13376 mr = 34451 m= 3007 mr = 10648 m= 349 mr = 2288 m= 13 mr = 215 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 5745 time to turn everything in is 2.090000 number of dielectric boundary points 80792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 15808 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) : 2.184988 object centre at (A) : 1.648999 15.16450 20.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2533288E-02 -1.174068 midg,1,midg; midg,igrid,midg -0.2414725 -0.1646503 1,midg,midg; igrid,midg,midg -0.2498512 -8.8048212E-02 gauss-seidel spectral radius is 0.9993110 estimated iterations to convergence 301 setup time was (sec) 2.410000 now iterating at: 11:47:03 rms-change max change #iterations 10.78425 401.0079 at 10iterations 6.334050 121.9680 at 20iterations 3.720590 61.61703 at 30iterations 2.187607 45.28868 at 40iterations 1.285475 19.99282 at 50iterations 0.7524083 14.13021 at 60iterations 0.4411494 7.186649 at 70iterations 0.2584146 4.476213 at 80iterations 0.1513707 2.790662 at 90iterations 8.8463821E-02 1.630682 at 100iterations 5.1835388E-02 0.9291992 at 110iterations 3.0404856E-02 0.4955363 at 120iterations 1.7765040E-02 0.3395252 at 130iterations 1.0387213E-02 0.1774024 at 140iterations 6.0902149E-03 9.7275734E-02 at 150iterations 3.5657617E-03 6.1495066E-02 at 160iterations 2.0917286E-03 3.4620166E-02 at 170iterations 1.2245466E-03 2.0954251E-02 at 180iterations finished qdiffx linear iterations at : 11:47:20 total time elapsed so far: 18.75000 # loops : 180 mean,max change (kT/e) : 1.2245466E-03 2.0954251E-02 energy calculations done at 18.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.92000 DelPhi exited at 11:47:20 18.926u 0.500s 0:19.71 98.5% 0+0k 0+0io 0pf+0w