Tue Oct 11 06:56:00 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 Tue Oct 11 2011 at 06:56:00 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 = 2966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5623657 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 0.5623657 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2827 net assigned charge : 0.5000190 assigned positive charge : 432.8355 centred at (gu) : 90.22060 90.13876 89.42841 assigned negative charge : -432.3362 centred at (gu) : 90.20202 90.25980 89.43397 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6189 nv = 96 ne = 84 npr = 60842 no. pairs analyzed = 60842 no. exposed pairs = 3771 no. arc points = 27077 no. surface atoms = 1285 nbur = 1681 mkacc time = 0.2000000 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 = 1.540000 m= 258 mr = 3211 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4400000 number of dielectric boundary points 3217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2722 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4385280E-10 -4.0046521E-12 midg,1,midg; midg,igrid,midg 1.4097398E-09 -1.4279873E-09 1,midg,midg; igrid,midg,midg -1.4969261E-10 2.9289324E-10 gauss-seidel spectral radius is 0.9836921 estimated iterations to convergence 64 setup time was (sec) 0.7900000 now iterating at: 06:56:01 rms-change max change #iterations 8.4333390E-02 13.45067 at 10iterations 6.0223076E-03 0.9816103 at 20iterations 4.7066479E-04 6.8090439E-02 at 30iterations 4.2343363E-05 7.2135925E-03 at 40iterations 5.5049027E-06 1.1281967E-03 at 50iterations finished qdiffx linear iterations at : 06:56:05 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 5.5049027E-06 1.1281967E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 06:56:06 4.842u 0.420s 0:05.79 90.8% 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 Tue Oct 11 2011 at 06:56:06 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 = 2966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.687097 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 1.687097 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2827 net assigned charge : 0.5000190 assigned positive charge : 432.8355 centred at (gu) : 90.66129 90.41582 88.28470 assigned negative charge : -432.3362 centred at (gu) : 90.60577 90.77911 88.30146 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 66951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27077 grid for indexing accessible points = 1.400000 m= 23109 mr = 44847 m= 2871 mr = 16673 m= 76 mr = 1600 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 544 time to turn everything in is 0.7800000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21822 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) : 0.5623657 object centre at (A) : 10.88300 49.15850 -46.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0499377E-03 1.3186445E-02 midg,1,midg; midg,igrid,midg -1.6767147E-03 -1.5908333E-04 1,midg,midg; igrid,midg,midg 4.0602256E-03 -8.1604086E-03 gauss-seidel spectral radius is 0.9983113 estimated iterations to convergence 193 setup time was (sec) 1.100000 now iterating at: 06:56:07 rms-change max change #iterations 3.493287 195.3576 at 10iterations 1.495862 56.26497 at 20iterations 0.6441396 23.06266 at 30iterations 0.2774211 10.58220 at 40iterations 0.1193340 4.143746 at 50iterations 5.1315218E-02 1.879969 at 60iterations 2.1975402E-02 0.7372093 at 70iterations 9.4944006E-03 0.3177986 at 80iterations 4.0960037E-03 0.1424484 at 90iterations 1.7620395E-03 5.8467865E-02 at 100iterations 7.6239539E-04 2.8409958E-02 at 110iterations 3.2912643E-04 1.1272430E-02 at 120iterations finished qdiffx linear iterations at : 06:56:17 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 3.2912643E-04 1.1272430E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 06:56:18 10.958u 0.490s 0:11.93 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 Tue Oct 11 2011 at 06:56:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.530646 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 2.530646 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2827 net assigned charge : 0.5000190 assigned positive charge : 432.8355 centred at (gu) : 90.99174 90.62367 87.42690 assigned negative charge : -432.3362 centred at (gu) : 90.90861 91.16867 87.45204 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 154941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27077 grid for indexing accessible points = 1.400000 m= 75749 mr = 109299 m= 25473 mr = 60841 m= 4730 mr = 20177 m= 317 mr = 3392 m= 1 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 1835 time to turn everything in is 1.760000 number of dielectric boundary points 67364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 22599 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) : 1.687097 object centre at (A) : 10.88300 49.15850 -46.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1089771 0.2331751 midg,1,midg; midg,igrid,midg 1.5600288E-07 1.3407415E-02 1,midg,midg; igrid,midg,midg -2.3567794E-02 -0.1689844 gauss-seidel spectral radius is 0.9991794 estimated iterations to convergence 276 setup time was (sec) 2.200000 now iterating at: 06:56:20 rms-change max change #iterations 8.913319 280.7825 at 10iterations 5.081763 146.7297 at 20iterations 2.887753 80.81448 at 30iterations 1.627124 39.49370 at 40iterations 0.9165068 19.11261 at 50iterations 0.5138727 11.32261 at 60iterations 0.2887290 6.375579 at 70iterations 0.1616172 3.566009 at 80iterations 9.0301633E-02 1.822678 at 90iterations 5.0469052E-02 1.036240 at 100iterations 2.8109314E-02 0.5876656 at 110iterations 1.5709927E-02 0.3434067 at 120iterations 8.7795518E-03 0.1662164 at 130iterations 4.9001151E-03 0.1004562 at 140iterations 2.7236668E-03 5.5342674E-02 at 150iterations 1.5194901E-03 3.2373428E-02 at 160iterations 8.4841426E-04 1.5738964E-02 at 170iterations 4.7335512E-04 9.2849731E-03 at 180iterations finished qdiffx linear iterations at : 06:56:36 total time elapsed so far: 18.15000 # loops : 180 mean,max change (kT/e) : 4.7335512E-04 9.2849731E-03 energy calculations done at 18.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.36000 DelPhi exited at 06:56:37 18.360u 0.534s 0:19.21 98.3% 0+0k 0+0io 0pf+0w