Sat Oct 15 12:54:02 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 Sat Oct 15 2011 at 12:54:02 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3787 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5151134 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): -41.78000 27.33100 ymin,ymax (A): 14.82200 74.21500 zmin,zma (A): 305.7490 364.3070 x,y,z range (A): 69.11100 59.39301 58.55801 scale (grids/A): 0.5151134 object centre (A): -7.224500 44.51850 335.0280 number of atom coordinates read : 3787 total number of charged atoms : 3634 net assigned charge : -6.999957 assigned positive charge : 546.9727 centred at (gu) : 89.38808 91.15976 90.51001 assigned negative charge : -553.9759 centred at (gu) : 89.48923 91.17313 90.47187 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6804 nv = 96 ne = 84 npr = 73683 no. pairs analyzed = 73683 no. exposed pairs = 5468 no. arc points = 37356 no. surface atoms = 1823 nbur = 1964 mkacc time = 0.2100000 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= 251 mr = 3171 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3725 ## 465 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8924 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8936196E-10 -3.4075791E-11 midg,1,midg; midg,igrid,midg -6.7712669E-11 -2.0959535E-10 1,midg,midg; igrid,midg,midg 1.4225789E-10 -3.1724484E-10 gauss-seidel spectral radius is 0.9806768 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 12:54:03 rms-change max change #iterations 6.0416020E-02 8.464386 at 10iterations 3.6794168E-03 0.6165810 at 20iterations 5.8767194E-04 0.1048594 at 30iterations 2.2725061E-04 4.2245865E-02 at 40iterations 9.3182025E-05 1.7319679E-02 at 50iterations finished qdiffx linear iterations at : 12:54:07 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 9.3182025E-05 1.7319679E-02 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 12:54:07 4.311u 0.309s 0:04.89 94.2% 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 12:54:07 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3787 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.545340 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): -41.78000 27.33100 ymin,ymax (A): 14.82200 74.21500 zmin,zma (A): 305.7490 364.3070 x,y,z range (A): 69.11100 59.39301 58.55801 scale (grids/A): 1.545340 object centre (A): -7.224500 44.51850 335.0280 number of atom coordinates read : 3787 total number of charged atoms : 3634 net assigned charge : -6.999957 assigned positive charge : 546.9727 centred at (gu) : 88.16261 93.47781 91.52861 assigned negative charge : -553.9759 centred at (gu) : 88.46733 93.51904 91.41538 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22597 mr = 48756 m= 2238 mr = 14409 m= 34 mr = 917 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.7000000 number of dielectric boundary points 36370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 391 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 27483 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) : 0.5151134 object centre at (A) : -7.224500 44.51850 335.0280 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4663033E-03 -6.6094293E-04 midg,1,midg; midg,igrid,midg -7.9084234E-03 -2.1526469E-03 1,midg,midg; igrid,midg,midg -4.6176696E-04 -3.7476108E-03 gauss-seidel spectral radius is 0.9980781 estimated iterations to convergence 181 setup time was (sec) 1.010000 now iterating at: 12:54:09 rms-change max change #iterations 3.337370 165.9026 at 10iterations 1.350004 47.73112 at 20iterations 0.5454454 18.88696 at 30iterations 0.2207547 7.724377 at 40iterations 8.9540362E-02 3.167084 at 50iterations 3.6457732E-02 1.223511 at 60iterations 1.4904060E-02 0.5165218 at 70iterations 6.1538448E-03 0.2163162 at 80iterations 2.6060285E-03 9.5348358E-02 at 90iterations 1.2044493E-03 4.4331074E-02 at 100iterations 6.3684536E-04 2.6273727E-02 at 110iterations 3.9419503E-04 1.4875412E-02 at 120iterations finished qdiffx linear iterations at : 12:54:17 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 3.9419503E-04 1.4875412E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 12:54:18 9.803u 0.331s 0:10.39 97.4% 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 12:54:18 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3787 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.318010 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): -41.78000 27.33100 ymin,ymax (A): 14.82200 74.21500 zmin,zma (A): 305.7490 364.3070 x,y,z range (A): 69.11100 59.39301 58.55801 scale (grids/A): 2.318010 object centre (A): -7.224500 44.51850 335.0280 number of atom coordinates read : 3787 total number of charged atoms : 3634 net assigned charge : -6.999957 assigned positive charge : 546.9727 centred at (gu) : 87.24371 95.21636 92.29274 assigned negative charge : -553.9759 centred at (gu) : 87.70107 95.27849 92.12312 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 175550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 78151 mr = 120830 m= 21693 mr = 58520 m= 3286 mr = 15466 m= 175 mr = 1972 m= 0 mr = 55 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 342 time to turn everything in is 1.710000 number of dielectric boundary points 82012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 29021 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) : 1.545340 object centre at (A) : -7.224500 44.51850 335.0280 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1404416 -1.6008841E-02 midg,1,midg; midg,igrid,midg -0.1499607 3.7215419E-02 1,midg,midg; igrid,midg,midg -0.1430077 1.9920046E-02 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 2.060000 now iterating at: 12:54:20 rms-change max change #iterations 9.109594 336.6731 at 10iterations 5.204363 176.3236 at 20iterations 2.937874 85.78793 at 30iterations 1.650344 33.83847 at 40iterations 0.9211065 18.53534 at 50iterations 0.5131257 10.46944 at 60iterations 0.2845668 6.245881 at 70iterations 0.1572842 2.887379 at 80iterations 8.6997710E-02 1.859073 at 90iterations 4.8067927E-02 0.9253101 at 100iterations 2.6537320E-02 0.5229793 at 110iterations 1.4652342E-02 0.3257141 at 120iterations 8.1017204E-03 0.1648235 at 130iterations 4.5057517E-03 9.5985413E-02 at 140iterations 2.5413302E-03 5.1246881E-02 at 150iterations 1.4688021E-03 3.1306267E-02 at 160iterations 8.8670495E-04 2.1553040E-02 at 170iterations 5.6957593E-04 1.2783051E-02 at 180iterations finished qdiffx linear iterations at : 12:54:34 total time elapsed so far: 16.42000 # loops : 180 mean,max change (kT/e) : 5.6957593E-04 1.2783051E-02 energy calculations done at 16.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.60000 DelPhi exited at 12:54:35 16.598u 0.323s 0:17.18 98.4% 0+0k 0+0io 0pf+0w