Mon Oct 10 16:58:03 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 Mon Oct 10 2011 at 16:58:04 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5592824 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 0.5592824 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 383.3669 centred at (gu) : 89.12698 91.07274 90.68196 assigned negative charge : -379.3678 centred at (gu) : 89.03343 91.01707 90.61005 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5295 nv = 96 ne = 84 npr = 51298 no. pairs analyzed = 51298 no. exposed pairs = 3432 no. arc points = 24520 no. surface atoms = 1151 nbur = 1428 mkacc time = 9.0000004E-02 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= 213 mr = 2609 m= 4 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2402 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1368764E-10 1.2588220E-09 midg,1,midg; midg,igrid,midg -7.6128617E-11 1.1931525E-09 1,midg,midg; igrid,midg,midg -5.7534477E-10 1.0221382E-09 gauss-seidel spectral radius is 0.9834812 estimated iterations to convergence 64 setup time was (sec) 0.3800000 now iterating at: 16:58:04 rms-change max change #iterations 7.7334933E-02 13.03781 at 10iterations 5.6337011E-03 1.006354 at 20iterations 5.2366836E-04 0.1072693 at 30iterations 8.6646134E-05 2.2012711E-02 at 40iterations 1.9835477E-05 5.1879883E-03 at 50iterations finished qdiffx linear iterations at : 16:58:07 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.9835477E-05 5.1879883E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 16:58:08 3.399u 0.177s 0:04.47 79.6% 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 16:58:08 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.677847 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 1.677847 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 383.3669 centred at (gu) : 87.38037 93.21748 92.04531 assigned negative charge : -379.3678 centred at (gu) : 87.10034 93.05088 91.83020 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18180 mr = 38293 m= 2037 mr = 12265 m= 54 mr = 945 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 26840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18772 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) : 0.5592824 object centre at (A) : 1.219501 5.141000 23.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9973809E-02 3.1407554E-02 midg,1,midg; midg,igrid,midg -1.6739916E-03 2.9273002E-04 1,midg,midg; igrid,midg,midg -9.8683368E-03 -1.5478997E-03 gauss-seidel spectral radius is 0.9982411 estimated iterations to convergence 189 setup time was (sec) 0.5200000 now iterating at: 16:58:09 rms-change max change #iterations 3.223783 176.8098 at 10iterations 1.353088 59.24956 at 20iterations 0.5723189 23.57038 at 30iterations 0.2426549 10.38019 at 40iterations 0.1023795 3.818920 at 50iterations 4.3256056E-02 1.736221 at 60iterations 1.8363560E-02 0.7079353 at 70iterations 7.8008589E-03 0.3177757 at 80iterations 3.3242065E-03 0.1206131 at 90iterations 1.4317873E-03 5.9808016E-02 at 100iterations 6.2983989E-04 2.4307251E-02 at 110iterations 2.8867376E-04 1.1865616E-02 at 120iterations finished qdiffx linear iterations at : 16:58:16 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.8867376E-04 1.1865616E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 16:58:17 7.679u 0.212s 0:08.47 93.0% 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 16:58:17 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.516771 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): -23.83500 26.27400 ymin,ymax (A): -19.69700 29.97900 zmin,zma (A): -8.271000 55.38200 x,y,z range (A): 50.10900 49.67600 63.65300 scale (grids/A): 2.516771 object centre (A): 1.219501 5.141000 23.55550 number of atom coordinates read : 2579 total number of charged atoms : 2440 net assigned charge : 4.000016 assigned positive charge : 383.3669 centred at (gu) : 86.07047 94.82625 93.06779 assigned negative charge : -379.3678 centred at (gu) : 85.65059 94.57636 92.74536 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 134945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24520 grid for indexing accessible points = 1.400000 m= 61880 mr = 94250 m= 18557 mr = 48212 m= 3135 mr = 13708 m= 240 mr = 1985 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 60524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 19505 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) : 1.677847 object centre at (A) : 1.219501 5.141000 23.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3498799 0.4006516 midg,1,midg; midg,igrid,midg -4.6632709E-03 -4.3951301E-03 1,midg,midg; igrid,midg,midg -0.1050089 -2.9071748E-02 gauss-seidel spectral radius is 0.9991481 estimated iterations to convergence 271 setup time was (sec) 0.9600000 now iterating at: 16:58:18 rms-change max change #iterations 8.232692 334.5876 at 10iterations 4.638763 116.3751 at 20iterations 2.587148 68.83259 at 30iterations 1.443203 32.52720 at 40iterations 0.8012667 17.72493 at 50iterations 0.4440573 10.97630 at 60iterations 0.2453572 6.111351 at 70iterations 0.1354742 3.014722 at 80iterations 7.4782588E-02 1.747553 at 90iterations 4.1268479E-02 0.9154937 at 100iterations 2.2795297E-02 0.4762535 at 110iterations 1.2539340E-02 0.2702503 at 120iterations 6.9238711E-03 0.1524773 at 130iterations 3.8191096E-03 7.6383591E-02 at 140iterations 2.1082184E-03 4.7218323E-02 at 150iterations 1.1646755E-03 2.5454998E-02 at 160iterations 6.4780388E-04 1.4846802E-02 at 170iterations 3.6127883E-04 7.8105927E-03 at 180iterations finished qdiffx linear iterations at : 16:58:29 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 3.6127883E-04 7.8105927E-03 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 16:58:30 12.241u 0.236s 0:12.97 96.1% 0+0k 0+0io 0pf+0w