Sat Oct 15 14:19:56 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 14:19:56 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 = 4795 !!! WARNING: HEM 819 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: 0.5102407 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 0.5102407 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4548 net assigned charge : 6.800033 assigned positive charge : 720.7173 centred at (gu) : 89.63892 90.45045 88.50709 assigned negative charge : -713.9219 centred at (gu) : 89.52811 90.52647 88.48395 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 96634 no. pairs analyzed = 96634 no. exposed pairs = 6078 no. arc points = 42499 no. surface atoms = 2029 nbur = 2766 mkacc time = 0.1700000 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= 270 mr = 4049 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4024 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10492 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5784453E-11 1.0657416E-10 midg,1,midg; midg,igrid,midg 2.5725724E-10 -1.1063393E-10 1,midg,midg; igrid,midg,midg -2.0794594E-10 3.4179384E-10 gauss-seidel spectral radius is 0.9803607 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 14:19:57 rms-change max change #iterations 6.8555489E-02 10.02856 at 10iterations 3.8383976E-03 0.6047726 at 20iterations 3.6208238E-04 5.1916122E-02 at 30iterations 1.1533727E-04 1.6998529E-02 at 40iterations 4.6026122E-05 6.8540573E-03 at 50iterations finished qdiffx linear iterations at : 14:20:00 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 4.6026122E-05 6.8540573E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:20:01 3.656u 0.200s 0:04.27 90.1% 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 14:20:01 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 = 4795 !!! WARNING: HEM 819 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: 1.530722 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 1.530722 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4548 net assigned charge : 6.800033 assigned positive charge : 720.7173 centred at (gu) : 88.91553 91.34980 85.51958 assigned negative charge : -713.9219 centred at (gu) : 88.58396 91.57907 85.45158 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25553 mr = 61872 m= 2170 mr = 16728 m= 45 mr = 880 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.4400000 number of dielectric boundary points 38453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 559 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34269 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) : 0.5102407 object centre at (A) : 10.34800 1.858002 30.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6647820E-03 2.0384954E-02 midg,1,midg; midg,igrid,midg 1.3484344E-02 -1.4465259E-02 1,midg,midg; igrid,midg,midg -9.4349083E-04 9.7554317E-03 gauss-seidel spectral radius is 0.9981140 estimated iterations to convergence 183 setup time was (sec) 0.6900000 now iterating at: 14:20:02 rms-change max change #iterations 3.810269 172.4292 at 10iterations 1.554913 59.11699 at 20iterations 0.6393017 23.95110 at 30iterations 0.2621599 8.162712 at 40iterations 0.1076650 3.360790 at 50iterations 4.4374593E-02 1.651820 at 60iterations 1.8207267E-02 0.6243443 at 70iterations 7.5054634E-03 0.2666826 at 80iterations 3.1195744E-03 9.7503662E-02 at 90iterations 1.3115881E-03 4.1336060E-02 at 100iterations 5.7330279E-04 1.9454360E-02 at 110iterations 2.7695825E-04 1.0056496E-02 at 120iterations finished qdiffx linear iterations at : 14:20:10 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 2.7695825E-04 1.0056496E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.690000 DelPhi exited at 14:20:10 8.691u 0.242s 0:09.33 95.7% 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 Sat Oct 15 2011 at 14:20:10 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 = 4795 !!! WARNING: HEM 819 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: 2.296083 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 2.296083 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4548 net assigned charge : 6.800033 assigned positive charge : 720.7173 centred at (gu) : 88.37307 92.02445 83.27916 assigned negative charge : -713.9219 centred at (gu) : 87.87588 92.36850 83.17726 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 210185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92794 mr = 152388 m= 22684 mr = 71957 m= 3150 mr = 15854 m= 175 mr = 1848 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 867 time to turn everything in is 1.130000 number of dielectric boundary points 86886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 36297 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) : 1.530722 object centre at (A) : 10.34800 1.858002 30.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1324034 0.5025999 midg,1,midg; midg,igrid,midg 0.2661701 -0.2983590 1,midg,midg; igrid,midg,midg -8.4079625E-03 0.1425501 gauss-seidel spectral radius is 0.9991654 estimated iterations to convergence 273 setup time was (sec) 1.410000 now iterating at: 14:20:12 rms-change max change #iterations 10.34343 301.6483 at 10iterations 5.922581 160.0829 at 20iterations 3.369552 76.86919 at 30iterations 1.907602 56.51941 at 40iterations 1.076827 21.29388 at 50iterations 0.6048155 13.06997 at 60iterations 0.3393522 6.617119 at 70iterations 0.1901483 4.684278 at 80iterations 0.1062167 1.951675 at 90iterations 5.9185639E-02 1.233240 at 100iterations 3.3067059E-02 0.6861396 at 110iterations 1.8439904E-02 0.3566360 at 120iterations 1.0264842E-02 0.1988087 at 130iterations 5.7161334E-03 0.1110001 at 140iterations 3.1840387E-03 5.9344113E-02 at 150iterations 1.7720632E-03 3.3874512E-02 at 160iterations 9.8950486E-04 1.8039703E-02 at 170iterations 5.5383006E-04 1.0810852E-02 at 180iterations finished qdiffx linear iterations at : 14:20:25 total time elapsed so far: 14.26000 # loops : 180 mean,max change (kT/e) : 5.5383006E-04 1.0810852E-02 energy calculations done at 14.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.40000 DelPhi exited at 14:20:25 14.398u 0.263s 0:15.08 97.1% 0+0k 0+0io 0pf+0w