Mon Oct 10 14:00:14 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 14:00:14 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5122744 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 0.5122744 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 710.3160 centred at (gu) : 90.31264 90.24717 88.81395 assigned negative charge : -700.3207 centred at (gu) : 90.24132 90.34287 88.89194 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7766 nv = 96 ne = 84 npr = 95263 no. pairs analyzed = 95263 no. exposed pairs = 5573 no. arc points = 38580 no. surface atoms = 1893 nbur = 2804 mkacc time = 0.2500000 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= 238 mr = 4146 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3923 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10474 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9334775E-10 -4.5868229E-11 midg,1,midg; midg,igrid,midg 3.8247183E-10 -1.2272831E-10 1,midg,midg; igrid,midg,midg -4.2150016E-11 3.7225983E-10 gauss-seidel spectral radius is 0.9805027 estimated iterations to convergence 59 setup time was (sec) 0.9200000 now iterating at: 14:00:17 rms-change max change #iterations 7.0734970E-02 11.29572 at 10iterations 5.1074959E-03 0.6771774 at 20iterations 9.7533013E-04 0.1451607 at 30iterations 3.2852218E-04 5.2810669E-02 at 40iterations 1.1842674E-04 1.9554138E-02 at 50iterations finished qdiffx linear iterations at : 14:00:25 total time elapsed so far: 8.390000 # loops : 50 mean,max change (kT/e) : 1.1842674E-04 1.9554138E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 14:00:26 8.584u 0.634s 0:11.53 79.8% 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 14:00:28 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.536823 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 1.536823 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 710.3160 centred at (gu) : 90.93661 90.74026 86.44032 assigned negative charge : -700.3207 centred at (gu) : 90.72359 91.02827 86.67558 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25250 mr = 62021 m= 2038 mr = 17200 m= 52 mr = 913 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 606 time to turn everything in is 0.7100000 number of dielectric boundary points 35802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 570 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 34132 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) : 0.5122744 object centre at (A) : -24.97600 -21.38600 -39.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4678843E-02 -1.0658192E-02 midg,1,midg; midg,igrid,midg 1.2759679E-02 -1.9506714E-03 1,midg,midg; igrid,midg,midg -1.7666498E-03 2.6368896E-02 gauss-seidel spectral radius is 0.9981128 estimated iterations to convergence 183 setup time was (sec) 1.000000 now iterating at: 14:00:30 rms-change max change #iterations 3.740472 151.2425 at 10iterations 1.530403 50.55132 at 20iterations 0.6298189 20.94201 at 30iterations 0.2581935 8.832462 at 40iterations 0.1063714 3.359615 at 50iterations 4.3874763E-02 1.506092 at 60iterations 1.8161356E-02 0.6397247 at 70iterations 7.6905694E-03 0.2455597 at 80iterations 3.3923236E-03 0.1071491 at 90iterations 1.6097357E-03 5.0567627E-02 at 100iterations 8.6306763E-04 3.1753540E-02 at 110iterations 5.2425981E-04 1.6105652E-02 at 120iterations finished qdiffx linear iterations at : 14:00:48 total time elapsed so far: 18.57000 # loops : 120 mean,max change (kT/e) : 5.2425981E-04 1.6105652E-02 energy calculations done at 18.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.76000 DelPhi exited at 14:00:48 18.760u 0.544s 0:19.81 97.4% 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 14:00:49 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.305235 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 2.305235 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 710.3160 centred at (gu) : 91.40431 91.10999 84.66017 assigned negative charge : -700.3207 centred at (gu) : 91.08523 91.54237 85.01329 start vw surface at 0.2200000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 206417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 91931 mr = 151844 m= 22191 mr = 72828 m= 2925 mr = 16195 m= 165 mr = 1842 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 2130 time to turn everything in is 2.140000 number of dielectric boundary points 80848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 36245 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) : 1.536823 object centre at (A) : -24.97600 -21.38600 -39.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5992983 -0.2412872 midg,1,midg; midg,igrid,midg 0.1962859 -2.8549789E-02 1,midg,midg; igrid,midg,midg 5.2915290E-03 0.5194478 gauss-seidel spectral radius is 0.9991565 estimated iterations to convergence 272 setup time was (sec) 2.780000 now iterating at: 14:00:52 rms-change max change #iterations 10.11958 281.1176 at 10iterations 5.780756 137.2672 at 20iterations 3.287950 76.05969 at 30iterations 1.856372 37.29420 at 40iterations 1.042845 21.06708 at 50iterations 0.5846831 11.27022 at 60iterations 0.3268049 6.524651 at 70iterations 0.1825585 3.545643 at 80iterations 0.1017883 1.930119 at 90iterations 5.6812443E-02 1.095255 at 100iterations 3.1605832E-02 0.6169224 at 110iterations 1.7587023E-02 0.4139810 at 120iterations 9.8095015E-03 0.1887207 at 130iterations 5.4853950E-03 0.1194687 at 140iterations 3.0790640E-03 5.5305481E-02 at 150iterations 1.7418744E-03 3.2512665E-02 at 160iterations 1.0003295E-03 1.9095421E-02 at 170iterations 5.8914570E-04 1.0902405E-02 at 180iterations finished qdiffx linear iterations at : 14:01:21 total time elapsed so far: 31.09000 # loops : 180 mean,max change (kT/e) : 5.8914570E-04 1.0902405E-02 energy calculations done at 31.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.29000 DelPhi exited at 14:01:22 31.292u 0.865s 0:33.32 96.4% 0+0k 0+0io 0pf+0w