Sat Oct 15 12:42:52 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 Sat Oct 15 2011 at 12:42:53 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 = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 0.4819016 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 0.4819016 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 863.6235 centred at (gu) : 89.89342 88.44747 89.23447 assigned negative charge : -862.6308 centred at (gu) : 89.73764 88.44023 89.14820 start vw surface at 0.2600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 8281 nv = 96 ne = 84 npr = 115000 no. pairs analyzed = 115000 no. exposed pairs = 7306 no. arc points = 51021 no. surface atoms = 2437 nbur = 3314 mkacc time = 0.5400000 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 = 1.792000 m= 255 mr = 4131 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.8900000 number of dielectric boundary points 4399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4735 ## 798 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 11260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6559621E-11 6.2280819E-11 midg,1,midg; midg,igrid,midg -2.4310695E-12 7.0528184E-12 1,midg,midg; igrid,midg,midg -1.3483675E-10 1.3037313E-10 gauss-seidel spectral radius is 0.9780601 estimated iterations to convergence 56 setup time was (sec) 1.200000 now iterating at: 12:42:56 rms-change max change #iterations 5.4521959E-02 8.289944 at 10iterations 2.7061945E-03 0.4023292 at 20iterations 2.1914222E-04 4.7021866E-02 at 30iterations 4.6957037E-05 1.0589600E-02 at 40iterations 1.3227010E-05 2.6817322E-03 at 50iterations finished qdiffx linear iterations at : 12:43:05 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 1.3227010E-05 2.6817322E-03 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.530000 DelPhi exited at 12:43:05 5.536u 0.434s 0:11.96 49.8% 0+0k 0+0io 5pf+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 Sat Oct 15 2011 at 12:43:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.445705 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 1.445705 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 863.6235 centred at (gu) : 89.67874 85.34075 87.70147 assigned negative charge : -862.6308 centred at (gu) : 89.21275 85.32045 87.44416 start vw surface at 0.2700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 94975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 24930 mr = 64276 m= 1691 mr = 15706 m= 35 mr = 590 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1741 time to turn everything in is 1.030000 number of dielectric boundary points 41059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 809 ## 14 charges are in solution ## iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 41010 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) : 0.4819016 object centre at (A) : 40.66500 54.19500 38.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6718461E-03 5.8838632E-03 midg,1,midg; midg,igrid,midg -9.5733342E-04 -2.5242928E-03 1,midg,midg; igrid,midg,midg -8.0884341E-03 2.0078026E-02 gauss-seidel spectral radius is 0.9979421 estimated iterations to convergence 175 setup time was (sec) 1.430000 now iterating at: 12:43:07 rms-change max change #iterations 3.648559 131.7415 at 10iterations 1.437568 48.19312 at 20iterations 0.5673844 17.91661 at 30iterations 0.2243106 7.596515 at 40iterations 8.8172801E-02 2.769028 at 50iterations 3.4827072E-02 1.166437 at 60iterations 1.3839466E-02 0.4547443 at 70iterations 5.4871095E-03 0.1854382 at 80iterations 2.1976989E-03 6.8486214E-02 at 90iterations 8.9257758E-04 3.3470154E-02 at 100iterations 3.7520812E-04 1.3639450E-02 at 110iterations 1.6991471E-04 6.2789917E-03 at 120iterations finished qdiffx linear iterations at : 12:43:27 total time elapsed so far: 11.96000 # loops : 120 mean,max change (kT/e) : 1.6991471E-04 6.2789917E-03 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 12:43:28 12.175u 0.551s 0:22.32 56.9% 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 Sat Oct 15 2011 at 12:43:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.168557 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 2.168557 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 863.6235 centred at (gu) : 89.51753 83.01070 86.55167 assigned negative charge : -862.6308 centred at (gu) : 88.81918 82.98054 86.16631 start vw surface at 0.2600000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 221970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 93576 mr = 159141 m= 20122 mr = 71117 m= 2097 mr = 13763 m= 68 mr = 1173 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 5686 time to turn everything in is 2.440000 number of dielectric boundary points 92626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 44446 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) : 1.445705 object centre at (A) : 40.66500 54.19500 38.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1286873 7.8966230E-02 midg,1,midg; midg,igrid,midg -1.6528925E-02 -3.7014328E-02 1,midg,midg; igrid,midg,midg -1.8593105E-02 0.3273763 gauss-seidel spectral radius is 0.9991381 estimated iterations to convergence 269 setup time was (sec) 2.880000 now iterating at: 12:43:37 rms-change max change #iterations 10.39075 268.5162 at 10iterations 5.945375 134.7658 at 20iterations 3.377823 68.92642 at 30iterations 1.901514 41.75271 at 40iterations 1.073936 23.81708 at 50iterations 0.5999566 14.01525 at 60iterations 0.3356394 8.683329 at 70iterations 0.1871781 3.609088 at 80iterations 0.1043118 2.090735 at 90iterations 5.8029138E-02 1.247092 at 100iterations 3.2230269E-02 0.6066990 at 110iterations 1.7837675E-02 0.4041977 at 120iterations 9.8961927E-03 0.1849365 at 130iterations 5.4838597E-03 0.1078135 at 140iterations 3.0317632E-03 5.7382584E-02 at 150iterations 1.6816563E-03 3.1390458E-02 at 160iterations 9.3289040E-04 1.6857147E-02 at 170iterations 5.1926414E-04 9.4604492E-03 at 180iterations finished qdiffx linear iterations at : 12:44:21 total time elapsed so far: 21.08000 # loops : 180 mean,max change (kT/e) : 5.1926414E-04 9.4604492E-03 energy calculations done at 21.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.30000 DelPhi exited at 12:44:22 21.309u 0.519s 0:54.04 40.3% 0+0k 0+0io 0pf+0w