Sun Oct 9 22:38:15 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 Sun Oct 9 2011 at 22:38:15 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4300 !!! WARNING: SEP 215 has a net charge of -0.4750 !!! WARNING: SEP 473 has a net charge of -0.4750 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: 0.5284486 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): 45.30500 112.6720 ymin,ymax (A): -16.73200 49.80900 zmin,zma (A): 1.069000 55.13500 x,y,z range (A): 67.36700 66.54100 54.06600 scale (grids/A): 0.5284486 object centre (A): 78.98850 16.53850 28.10200 number of atom coordinates read : 4300 total number of charged atoms : 4138 net assigned charge : 5.050012 assigned positive charge : 654.6773 centred at (gu) : 90.11625 89.86028 90.32055 assigned negative charge : -649.6316 centred at (gu) : 90.11954 89.88752 90.14646 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7727 nv = 96 ne = 84 npr = 85035 no. pairs analyzed = 85035 no. exposed pairs = 5625 no. arc points = 39355 no. surface atoms = 1904 nbur = 2396 mkacc time = 0.1500000 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= 294 mr = 3945 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3931 ## 600 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10381 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6844219E-10 1.0784452E-09 midg,1,midg; midg,igrid,midg 2.9670974E-10 1.7036561E-11 1,midg,midg; igrid,midg,midg 1.6380015E-10 1.4008547E-10 gauss-seidel spectral radius is 0.9816552 estimated iterations to convergence 61 setup time was (sec) 0.4800000 now iterating at: 22:38:16 rms-change max change #iterations 7.5988218E-02 13.19306 at 10iterations 4.8253750E-03 0.7019429 at 20iterations 3.9984178E-04 7.5889587E-02 at 30iterations 1.0142258E-04 2.4414063E-02 at 40iterations 3.6892903E-05 8.9964867E-03 at 50iterations finished qdiffx linear iterations at : 22:38:19 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.6892903E-05 8.9964867E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 22:38:19 3.514u 0.176s 0:03.99 92.2% 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 Sun Oct 9 2011 at 22:38:19 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4300 !!! WARNING: SEP 215 has a net charge of -0.4750 !!! WARNING: SEP 473 has a net charge of -0.4750 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: 1.585346 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): 45.30500 112.6720 ymin,ymax (A): -16.73200 49.80900 zmin,zma (A): 1.069000 55.13500 x,y,z range (A): 67.36700 66.54100 54.06600 scale (grids/A): 1.585346 object centre (A): 78.98850 16.53850 28.10200 number of atom coordinates read : 4300 total number of charged atoms : 4138 net assigned charge : 5.050012 assigned positive charge : 654.6773 centred at (gu) : 90.34732 89.57912 90.95996 assigned negative charge : -649.6316 centred at (gu) : 90.35812 89.66221 90.43909 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 24873 mr = 58509 m= 2188 mr = 16491 m= 42 mr = 1031 m= 1 mr = 7 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 0.4200000 number of dielectric boundary points 38154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 31401 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) : 0.5284486 object centre at (A) : 78.98850 16.53850 28.10200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8199038E-02 1.0731175E-03 midg,1,midg; midg,igrid,midg 2.4926653E-02 1.6418073E-02 1,midg,midg; igrid,midg,midg 2.7820056E-02 2.5597801E-02 gauss-seidel spectral radius is 0.9982179 estimated iterations to convergence 188 setup time was (sec) 0.6400000 now iterating at: 22:38:20 rms-change max change #iterations 3.877879 153.4159 at 10iterations 1.624443 53.71999 at 20iterations 0.6825227 25.92385 at 30iterations 0.2852600 9.422199 at 40iterations 0.1197708 4.104717 at 50iterations 5.0507411E-02 1.526705 at 60iterations 2.1257086E-02 0.7620901 at 70iterations 8.9263124E-03 0.2982875 at 80iterations 3.7587858E-03 0.1227722 at 90iterations 1.5814961E-03 4.8088074E-02 at 100iterations 6.7745685E-04 2.0978928E-02 at 110iterations 2.9455870E-04 1.0295868E-02 at 120iterations finished qdiffx linear iterations at : 22:38:27 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.9455870E-04 1.0295868E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 22:38:28 7.944u 0.202s 0:08.49 95.8% 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 Sun Oct 9 2011 at 22:38:28 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4300 !!! WARNING: SEP 215 has a net charge of -0.4750 !!! WARNING: SEP 473 has a net charge of -0.4750 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: 2.378019 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): 45.30500 112.6720 ymin,ymax (A): -16.73200 49.80900 zmin,zma (A): 1.069000 55.13500 x,y,z range (A): 67.36700 66.54100 54.06600 scale (grids/A): 2.378019 object centre (A): 78.98850 16.53850 28.10200 number of atom coordinates read : 4300 total number of charged atoms : 4138 net assigned charge : 5.050012 assigned positive charge : 654.6773 centred at (gu) : 90.52045 89.36829 91.43978 assigned negative charge : -649.6316 centred at (gu) : 90.53695 89.49308 90.65849 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 202844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 88949 mr = 143753 m= 22265 mr = 69301 m= 3238 mr = 16054 m= 211 mr = 2128 m= 6 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 86178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 33044 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) : 1.585346 object centre at (A) : 78.98850 16.53850 28.10200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2335803 -2.1394527E-02 midg,1,midg; midg,igrid,midg 0.4575250 0.3755101 1,midg,midg; igrid,midg,midg 0.8204939 0.8855988 gauss-seidel spectral radius is 0.9991865 estimated iterations to convergence 277 setup time was (sec) 1.280000 now iterating at: 22:38:29 rms-change max change #iterations 10.42548 274.0108 at 10iterations 6.084664 152.3021 at 20iterations 3.505349 81.06381 at 30iterations 2.007653 45.49760 at 40iterations 1.145053 25.64822 at 50iterations 0.6499766 13.37247 at 60iterations 0.3683981 7.491287 at 70iterations 0.2080810 4.666428 at 80iterations 0.1170083 2.591095 at 90iterations 6.6007316E-02 1.163940 at 100iterations 3.7105761E-02 0.6486230 at 110iterations 2.0829357E-02 0.3992543 at 120iterations 1.1692480E-02 0.2168474 at 130iterations 6.5623117E-03 0.1277142 at 140iterations 3.6822138E-03 6.5466881E-02 at 150iterations 2.0755273E-03 4.0145874E-02 at 160iterations 1.1729033E-03 2.1684647E-02 at 170iterations 6.6767627E-04 1.3683319E-02 at 180iterations finished qdiffx linear iterations at : 22:38:41 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 6.6767627E-04 1.3683319E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 22:38:41 13.011u 0.205s 0:13.64 96.8% 0+0k 0+0io 0pf+0w