Mon Oct 10 16:59:19 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 16:59:19 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5142279 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 0.5142279 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 608.9968 centred at (gu) : 90.34776 90.80426 87.07323 assigned negative charge : -605.7001 centred at (gu) : 90.20184 90.85459 87.07384 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6837 nv = 96 ne = 84 npr = 84790 no. pairs analyzed = 84790 no. exposed pairs = 5326 no. arc points = 37244 no. surface atoms = 1780 nbur = 2349 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 = 1.652000 m= 237 mr = 3440 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3535 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1912946E-10 2.5390053E-11 midg,1,midg; midg,igrid,midg 1.4669288E-10 -9.2526022E-11 1,midg,midg; igrid,midg,midg -2.9409589E-10 4.5715262E-10 gauss-seidel spectral radius is 0.9806125 estimated iterations to convergence 59 setup time was (sec) 0.4600000 now iterating at: 16:59:20 rms-change max change #iterations 6.5764956E-02 14.09064 at 10iterations 3.6215561E-03 0.5853615 at 20iterations 2.5751579E-04 3.4368515E-02 at 30iterations 4.8695503E-05 6.8941116E-03 at 40iterations 1.5678672E-05 2.2537708E-03 at 50iterations finished qdiffx linear iterations at : 16:59:22 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.5678672E-05 2.2537708E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:59:23 3.464u 0.198s 0:04.42 82.5% 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 16:59:23 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.542684 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 1.542684 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 608.9968 centred at (gu) : 91.04212 92.41145 81.21845 assigned negative charge : -605.7001 centred at (gu) : 90.60509 92.56361 81.22139 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 21944 mr = 51879 m= 1913 mr = 14344 m= 52 mr = 797 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3700000 number of dielectric boundary points 33991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 462 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 29261 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) : 0.5142279 object centre at (A) : 10.80150 0.5474997 30.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3953121E-03 7.1289572E-03 midg,1,midg; midg,igrid,midg -2.6075070E-04 -1.0092576E-02 1,midg,midg; igrid,midg,midg -2.4443949E-03 9.9644763E-03 gauss-seidel spectral radius is 0.9980778 estimated iterations to convergence 181 setup time was (sec) 0.5900000 now iterating at: 16:59:24 rms-change max change #iterations 3.487142 157.3389 at 10iterations 1.410644 49.86495 at 20iterations 0.5741804 19.10434 at 30iterations 0.2332147 10.21850 at 40iterations 9.4617248E-02 3.481499 at 50iterations 3.8574345E-02 1.238190 at 60iterations 1.5621294E-02 0.5372162 at 70iterations 6.3968939E-03 0.2040749 at 80iterations 2.5944882E-03 8.7778807E-02 at 90iterations 1.0619391E-03 3.8984299E-02 at 100iterations 4.3187803E-04 1.4717102E-02 at 110iterations 1.7747148E-04 6.2389374E-03 at 120iterations finished qdiffx linear iterations at : 16:59:31 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.7747148E-04 6.2389374E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 16:59:32 7.761u 0.211s 0:08.69 91.7% 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 16:59:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.314026 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 2.314026 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 608.9968 centred at (gu) : 91.56292 93.61674 76.82734 assigned negative charge : -605.7001 centred at (gu) : 90.90761 93.84522 76.83198 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 78277 mr = 127711 m= 19533 mr = 60355 m= 2807 mr = 13799 m= 144 mr = 1714 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.9400000 number of dielectric boundary points 76801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 31024 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) : 1.542684 object centre at (A) : 10.80150 0.5474997 30.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1349931 0.2289784 midg,1,midg; midg,igrid,midg -6.2344108E-02 -0.2531371 1,midg,midg; igrid,midg,midg -2.1638582E-02 0.1505053 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 1.180000 now iterating at: 16:59:34 rms-change max change #iterations 9.463965 326.9174 at 10iterations 5.364146 133.1752 at 20iterations 3.017139 76.75037 at 30iterations 1.692166 41.18629 at 40iterations 0.9477085 20.43330 at 50iterations 0.5270151 13.13153 at 60iterations 0.2934689 7.557641 at 70iterations 0.1621245 3.887367 at 80iterations 8.9806058E-02 2.035976 at 90iterations 4.9617756E-02 1.005636 at 100iterations 2.7397953E-02 0.6225142 at 110iterations 1.5132192E-02 0.3221130 at 120iterations 8.3420649E-03 0.1869383 at 130iterations 4.5959041E-03 9.1993332E-02 at 140iterations 2.5294756E-03 5.4734826E-02 at 150iterations 1.3966333E-03 2.9248238E-02 at 160iterations 7.6959236E-04 1.6075134E-02 at 170iterations 4.2363338E-04 8.6092949E-03 at 180iterations finished qdiffx linear iterations at : 16:59:46 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 4.2363338E-04 8.6092949E-03 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 16:59:46 12.898u 0.230s 0:13.91 94.3% 0+0k 0+0io 0pf+0w