Sat Oct 15 15:14:33 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 15:14:34 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 = 2789 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6637704 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 0.6637704 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2642 net assigned charge : 5.500012 assigned positive charge : 422.7236 centred at (gu) : 89.95403 91.60950 90.41904 assigned negative charge : -417.2243 centred at (gu) : 89.69002 91.45556 90.54163 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8221 nv = 96 ne = 84 npr = 57137 no. pairs analyzed = 57137 no. exposed pairs = 3368 no. arc points = 23491 no. surface atoms = 1137 nbur = 1652 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 502 mr = 4667 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2900000 number of dielectric boundary points 3998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2339 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9765929E-08 -1.5299511E-08 midg,1,midg; midg,igrid,midg -1.5109334E-08 7.0737258E-08 1,midg,midg; igrid,midg,midg -4.8823981E-08 7.4365254E-08 gauss-seidel spectral radius is 0.9882497 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 15:14:34 rms-change max change #iterations 0.1778527 25.45183 at 10iterations 1.9451426E-02 2.505548 at 20iterations 2.0896818E-03 0.2661533 at 30iterations 2.2870261E-04 3.2287598E-02 at 40iterations 2.6277319E-05 3.7317276E-03 at 50iterations finished qdiffx linear iterations at : 15:14:38 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 2.6277319E-05 3.7317276E-03 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 15:14:39 4.431u 0.273s 0:04.99 94.1% 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 15:14:39 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 = 2789 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991311 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 1.991311 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2642 net assigned charge : 5.500012 assigned positive charge : 422.7236 centred at (gu) : 89.86144 94.82818 91.25667 assigned negative charge : -417.2243 centred at (gu) : 89.06963 94.36650 91.62483 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23491 grid for indexing accessible points = 1.400000 m= 32848 mr = 61752 m= 5783 mr = 24541 m= 439 mr = 3645 m= 4 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 328 time to turn everything in is 0.6700000 number of dielectric boundary points 36548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20884 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) : 0.6637704 object centre at (A) : 18.93000 23.02200 67.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1818449E-02 -2.2640008E-02 midg,1,midg; midg,igrid,midg -1.7989378E-03 2.9917695E-02 1,midg,midg; igrid,midg,midg -2.8900903E-02 8.1336953E-02 gauss-seidel spectral radius is 0.9987632 estimated iterations to convergence 225 setup time was (sec) 1.010000 now iterating at: 15:14:40 rms-change max change #iterations 4.814924 200.9543 at 10iterations 2.329181 76.78439 at 20iterations 1.136336 34.57568 at 30iterations 0.5511987 17.09239 at 40iterations 0.2678612 7.589968 at 50iterations 0.1299864 3.670736 at 60iterations 6.3218065E-02 2.038923 at 70iterations 3.0769529E-02 0.9089298 at 80iterations 1.5046774E-02 0.4559002 at 90iterations 7.2966027E-03 0.1924672 at 100iterations 3.5434915E-03 0.1049480 at 110iterations 1.7260633E-03 5.2145958E-02 at 120iterations finished qdiffx linear iterations at : 15:14:49 total time elapsed so far: 9.970000 # loops : 120 mean,max change (kT/e) : 1.7260633E-03 5.2145958E-02 energy calculations done at 9.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 15:14:49 10.163u 0.285s 0:10.73 97.2% 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 Sat Oct 15 2011 at 15:14:49 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 = 2789 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.986967 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 2.986967 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2642 net assigned charge : 5.500012 assigned positive charge : 422.7236 centred at (gu) : 89.79216 97.24220 91.88467 assigned negative charge : -417.2243 centred at (gu) : 88.60440 96.54966 92.43716 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 202496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23491 grid for indexing accessible points = 1.400000 m= 105116 mr = 149315 m= 39922 mr = 86748 m= 10569 mr = 32360 m= 1836 mr = 7949 m= 134 mr = 1243 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 1271 time to turn everything in is 1.730000 number of dielectric boundary points 82403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 21136 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) : 1.991311 object centre at (A) : 18.93000 23.02200 67.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2565610 -0.2859048 midg,1,midg; midg,igrid,midg 4.1030981E-02 9.3459517E-02 1,midg,midg; igrid,midg,midg -0.3019070 0.8158795 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 2.090000 now iterating at: 15:14:52 rms-change max change #iterations 10.97294 446.2029 at 10iterations 6.443360 139.0331 at 20iterations 3.787464 71.01496 at 30iterations 2.221981 41.57785 at 40iterations 1.299302 21.55237 at 50iterations 0.7599991 13.00500 at 60iterations 0.4439428 7.437881 at 70iterations 0.2591009 4.702387 at 80iterations 0.1512266 2.583071 at 90iterations 8.8240050E-02 1.744683 at 100iterations 5.1309608E-02 0.9598928 at 110iterations 2.9863741E-02 0.4879881 at 120iterations 1.7380480E-02 0.2831254 at 130iterations 1.0133263E-02 0.1722546 at 140iterations 5.9237084E-03 9.3872070E-02 at 150iterations 3.4671847E-03 6.1437607E-02 at 160iterations 2.0375124E-03 3.8696289E-02 at 170iterations 1.2077671E-03 2.1841049E-02 at 180iterations finished qdiffx linear iterations at : 15:15:06 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 1.2077671E-03 2.1841049E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 15:15:07 16.646u 0.299s 0:17.23 98.2% 0+0k 0+0io 0pf+0w