Mon Oct 10 14:13:03 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 14:13:04 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 = 3365 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: 0.5110904 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 0.5110904 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500014 assigned positive charge : 517.9721 centred at (gu) : 88.99754 89.01663 91.18348 assigned negative charge : -513.4734 centred at (gu) : 88.95280 89.04923 91.13065 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5637 nv = 96 ne = 84 npr = 64264 no. pairs analyzed = 64264 no. exposed pairs = 4667 no. arc points = 33603 no. surface atoms = 1551 nbur = 1814 mkacc time = 0.1400000 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= 189 mr = 2536 m= 0 mr = 3 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3407 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6329364E-11 2.2370604E-10 midg,1,midg; midg,igrid,midg 1.6265153E-10 2.0248109E-12 1,midg,midg; igrid,midg,midg -2.9035515E-11 1.1426891E-10 gauss-seidel spectral radius is 0.9803296 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 14:13:04 rms-change max change #iterations 5.4089975E-02 10.79658 at 10iterations 3.4601390E-03 0.6517563 at 20iterations 4.7365139E-04 0.1164608 at 30iterations 1.0530815E-04 2.7267456E-02 at 40iterations 2.5052532E-05 6.4277649E-03 at 50iterations finished qdiffx linear iterations at : 14:13:07 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.5052532E-05 6.4277649E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:13:08 3.480u 0.212s 0:04.17 88.4% 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 14:13:08 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 = 3365 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: 1.533271 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 1.533271 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500014 assigned positive charge : 517.9721 centred at (gu) : 86.99137 87.04880 93.54955 assigned negative charge : -513.4734 centred at (gu) : 86.85810 87.14733 93.39125 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15958 mr = 39214 m= 1222 mr = 9588 m= 24 mr = 424 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 459 time to turn everything in is 0.4500000 number of dielectric boundary points 30610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 577 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 24237 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) : 0.5110904 object centre at (A) : 10.85650 6.659499 23.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7408158E-03 8.1373779E-03 midg,1,midg; midg,igrid,midg 3.7344741E-03 -2.1045627E-03 1,midg,midg; igrid,midg,midg -2.4172524E-03 1.4766655E-03 gauss-seidel spectral radius is 0.9979783 estimated iterations to convergence 177 setup time was (sec) 0.7500000 now iterating at: 14:13:09 rms-change max change #iterations 3.105419 148.9355 at 10iterations 1.229376 60.21274 at 20iterations 0.4874851 17.82063 at 30iterations 0.1933979 8.299295 at 40iterations 7.6655060E-02 2.859782 at 50iterations 3.0521471E-02 1.202253 at 60iterations 1.2261412E-02 0.4434090 at 70iterations 4.9513029E-03 0.2089348 at 80iterations 2.0440754E-03 9.4987869E-02 at 90iterations 8.8582636E-04 4.0725708E-02 at 100iterations 4.1165052E-04 1.9302368E-02 at 110iterations 2.0875454E-04 1.0730743E-02 at 120iterations finished qdiffx linear iterations at : 14:13:15 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 2.0875454E-04 1.0730743E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 14:13:16 7.448u 0.224s 0:08.17 93.7% 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 14:13:16 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 = 3365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.299907 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 2.299907 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500014 assigned positive charge : 517.9721 centred at (gu) : 85.48671 85.57289 95.32408 assigned negative charge : -513.4734 centred at (gu) : 85.28699 85.72076 95.08674 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 145535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 58419 mr = 97272 m= 13172 mr = 42972 m= 1696 mr = 8707 m= 93 mr = 919 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.040000 number of dielectric boundary points 69018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 25670 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) : 1.533271 object centre at (A) : 10.85650 6.659499 23.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2223841 0.1599467 midg,1,midg; midg,igrid,midg 4.9814045E-02 -3.2202691E-02 1,midg,midg; igrid,midg,midg -2.6991656E-03 4.5988909E-03 gauss-seidel spectral radius is 0.9990913 estimated iterations to convergence 262 setup time was (sec) 1.350000 now iterating at: 14:13:17 rms-change max change #iterations 8.621064 303.5956 at 10iterations 4.858498 147.2357 at 20iterations 2.711677 71.57639 at 30iterations 1.503519 35.76346 at 40iterations 0.8283882 20.17994 at 50iterations 0.4552589 11.21356 at 60iterations 0.2493571 5.702674 at 70iterations 0.1364335 3.161451 at 80iterations 7.4157499E-02 1.779658 at 90iterations 4.0428173E-02 0.9620132 at 100iterations 2.2018792E-02 0.4827633 at 110iterations 1.1966104E-02 0.2814388 at 120iterations 6.5145474E-03 0.1508789 at 130iterations 3.5547721E-03 7.6350689E-02 at 140iterations 1.9499880E-03 4.2650223E-02 at 150iterations 1.0776805E-03 2.4894714E-02 at 160iterations 6.0306053E-04 1.4274597E-02 at 170iterations 3.4557359E-04 8.5906982E-03 at 180iterations finished qdiffx linear iterations at : 14:13:28 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 3.4557359E-04 8.5906982E-03 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 14:13:29 11.822u 0.221s 0:12.68 94.9% 0+0k 0+0io 0pf+0w