Mon Oct 10 14:09:52 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 Mon Oct 10 2011 at 14:09:52 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 = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5413461 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 0.5413461 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2562 net assigned charge : 5.000004 assigned positive charge : 408.7424 centred at (gu) : 90.32272 91.01070 89.22078 assigned negative charge : -403.7434 centred at (gu) : 90.21780 90.88697 89.32611 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5229 nv = 96 ne = 84 npr = 52948 no. pairs analyzed = 52948 no. exposed pairs = 3542 no. arc points = 25240 no. surface atoms = 1190 nbur = 1511 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 = 1.596000 m= 223 mr = 2570 m= 0 mr = 17 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3500000 number of dielectric boundary points 2865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2576 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3936103E-10 -2.3977095E-10 midg,1,midg; midg,igrid,midg -2.9995068E-10 1.1129716E-09 1,midg,midg; igrid,midg,midg -2.6834723E-10 8.3527302E-10 gauss-seidel spectral radius is 0.9823927 estimated iterations to convergence 62 setup time was (sec) 0.6200000 now iterating at: 14:09:53 rms-change max change #iterations 6.7862056E-02 12.72318 at 10iterations 4.3451511E-03 0.7429550 at 20iterations 3.0622489E-04 5.5282593E-02 at 30iterations 3.1834548E-05 4.9934387E-03 at 40iterations 6.2138461E-06 1.0299683E-03 at 50iterations finished qdiffx linear iterations at : 14:09:56 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 6.2138461E-06 1.0299683E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:09:57 4.019u 0.237s 0:04.67 90.7% 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 Mon Oct 10 2011 at 14:09:57 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 = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.624038 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 1.624038 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2562 net assigned charge : 5.000004 assigned positive charge : 408.7424 centred at (gu) : 90.96762 93.03146 87.66155 assigned negative charge : -403.7434 centred at (gu) : 90.65321 92.66071 87.97807 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 57770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25240 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17740 mr = 38402 m= 1811 mr = 11778 m= 38 mr = 782 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 234 time to turn everything in is 0.5400000 number of dielectric boundary points 26397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19628 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) : 0.5413461 object centre at (A) : 24.01600 14.57250 15.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6039032E-02 4.6177185E-03 midg,1,midg; midg,igrid,midg 8.5640507E-04 1.0446645E-02 1,midg,midg; igrid,midg,midg -1.7244000E-02 2.8027683E-03 gauss-seidel spectral radius is 0.9981451 estimated iterations to convergence 184 setup time was (sec) 0.8400000 now iterating at: 14:09:58 rms-change max change #iterations 3.086818 146.7376 at 10iterations 1.275083 55.39309 at 20iterations 0.5235654 22.04688 at 30iterations 0.2154025 8.379422 at 40iterations 8.8624351E-02 3.359787 at 50iterations 3.6762062E-02 1.407313 at 60iterations 1.5179965E-02 0.6251457 at 70iterations 6.2532928E-03 0.2400484 at 80iterations 2.5861058E-03 0.1036415 at 90iterations 1.0677307E-03 3.8740158E-02 at 100iterations 4.4309371E-04 1.9489288E-02 at 110iterations 1.8361845E-04 7.2422028E-03 at 120iterations finished qdiffx linear iterations at : 14:10:06 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 1.8361845E-04 7.2422028E-03 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 14:10:07 8.984u 0.246s 0:10.03 91.9% 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 Mon Oct 10 2011 at 14:10:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.436058 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 2.436058 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2562 net assigned charge : 5.000004 assigned positive charge : 408.7424 centred at (gu) : 91.45130 94.54716 86.49220 assigned negative charge : -403.7434 centred at (gu) : 90.97970 93.99113 86.96708 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 134091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25240 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61286 mr = 94188 m= 17077 mr = 47518 m= 2726 mr = 12399 m= 198 mr = 1654 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 945 time to turn everything in is 1.250000 number of dielectric boundary points 59528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20468 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) : 1.624038 object centre at (A) : 24.01600 14.57250 15.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6877247 0.1347539 midg,1,midg; midg,igrid,midg 3.1019302E-02 0.1176539 1,midg,midg; igrid,midg,midg -0.3059112 3.3366013E-02 gauss-seidel spectral radius is 0.9991191 estimated iterations to convergence 266 setup time was (sec) 1.550000 now iterating at: 14:10:09 rms-change max change #iterations 8.132941 346.9525 at 10iterations 4.577460 134.8875 at 20iterations 2.563357 66.91922 at 30iterations 1.421282 34.28979 at 40iterations 0.7866913 19.88749 at 50iterations 0.4338910 11.46535 at 60iterations 0.2388835 5.767656 at 70iterations 0.1312915 3.189506 at 80iterations 7.2001912E-02 1.855803 at 90iterations 3.9525703E-02 0.8482819 at 100iterations 2.1643138E-02 0.4737244 at 110iterations 1.1855286E-02 0.2898521 at 120iterations 6.4847893E-03 0.1415949 at 130iterations 3.5472431E-03 7.6288223E-02 at 140iterations 1.9385320E-03 4.2829514E-02 at 150iterations 1.0607245E-03 2.3776054E-02 at 160iterations 5.8048725E-04 1.2636662E-02 at 170iterations 3.1693644E-04 6.6056252E-03 at 180iterations finished qdiffx linear iterations at : 14:10:22 total time elapsed so far: 14.55000 # loops : 180 mean,max change (kT/e) : 3.1693644E-04 6.6056252E-03 energy calculations done at 14.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.72000 DelPhi exited at 14:10:23 14.725u 0.306s 0:15.77 95.2% 0+0k 0+0io 0pf+0w