Mon Oct 10 23:53:25 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 23:53:25 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 = 2577 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: 0.5781849 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 0.5781849 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2436 net assigned charge : 5.000012 assigned positive charge : 385.1497 centred at (gu) : 89.06957 89.12770 90.08688 assigned negative charge : -380.1505 centred at (gu) : 89.00330 89.30884 89.97278 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5630 nv = 96 ne = 84 npr = 52791 no. pairs analyzed = 52791 no. exposed pairs = 2977 no. arc points = 20965 no. surface atoms = 1003 nbur = 1574 mkacc time = 0.1400000 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 = 1.484000 m= 222 mr = 3147 m= 0 mr = 19 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.3100000 number of dielectric boundary points 2686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2105 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0180037E-09 3.0629193E-09 midg,1,midg; midg,igrid,midg 5.1005311E-09 -1.8356080E-09 1,midg,midg; igrid,midg,midg -2.3305444E-10 1.7499575E-09 gauss-seidel spectral radius is 0.9845236 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 23:53:26 rms-change max change #iterations 9.2740506E-02 14.83617 at 10iterations 7.9437587E-03 1.270950 at 20iterations 1.0317080E-03 0.2254066 at 30iterations 2.2610593E-04 5.4985046E-02 at 40iterations 5.5583507E-05 1.3744354E-02 at 50iterations finished qdiffx linear iterations at : 23:53:30 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 5.5583507E-05 1.3744354E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 23:53:30 4.492u 0.387s 0:05.21 93.4% 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 Mon Oct 10 2011 at 23:53:31 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 = 2577 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: 1.734555 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 1.734555 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2436 net assigned charge : 5.000012 assigned positive charge : 385.1497 centred at (gu) : 87.20827 87.38235 90.26007 assigned negative charge : -380.1505 centred at (gu) : 87.00967 87.92637 89.91797 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 20468 mr = 43906 m= 2495 mr = 15062 m= 67 mr = 1484 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2749 time to turn everything in is 0.5100000 number of dielectric boundary points 24893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18890 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) : 0.5781849 object centre at (A) : 40.87750 46.90100 43.88650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7846277E-03 1.4017206E-02 midg,1,midg; midg,igrid,midg -7.8277262E-03 -2.3909371E-02 1,midg,midg; igrid,midg,midg 1.6332408E-03 1.3628424E-02 gauss-seidel spectral radius is 0.9983498 estimated iterations to convergence 195 setup time was (sec) 0.7800000 now iterating at: 23:53:32 rms-change max change #iterations 3.478116 168.4903 at 10iterations 1.507057 53.99125 at 20iterations 0.6547371 24.33505 at 30iterations 0.2851273 11.03102 at 40iterations 0.1236302 4.784997 at 50iterations 5.3838108E-02 2.014381 at 60iterations 2.3612481E-02 0.8029022 at 70iterations 1.0421985E-02 0.4236412 at 80iterations 4.6708398E-03 0.1912289 at 90iterations 2.1583240E-03 8.9736938E-02 at 100iterations 1.0673122E-03 4.6913147E-02 at 110iterations 5.6769588E-04 2.4936676E-02 at 120iterations finished qdiffx linear iterations at : 23:53:41 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 5.6769588E-04 2.4936676E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.20000 DelPhi exited at 23:53:42 10.206u 0.480s 0:11.22 95.1% 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 Mon Oct 10 2011 at 23:53:42 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 = 2577 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: 2.601832 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): 13.95000 67.80500 ymin,ymax (A): 16.11500 77.68700 zmin,zma (A): 23.13800 64.63500 x,y,z range (A): 53.85500 61.57200 41.49700 scale (grids/A): 2.601832 object centre (A): 40.87750 46.90100 43.88650 number of atom coordinates read : 2577 total number of charged atoms : 2436 net assigned charge : 5.000012 assigned positive charge : 385.1497 centred at (gu) : 85.81209 86.07346 90.38995 assigned negative charge : -380.1505 centred at (gu) : 85.51449 86.88944 89.87690 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 144678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 69667 mr = 106622 m= 21881 mr = 57346 m= 4196 mr = 17419 m= 335 mr = 3135 m= 8 mr = 187 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 9192 time to turn everything in is 1.240000 number of dielectric boundary points 56056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19473 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) : 1.734555 object centre at (A) : 40.87750 46.90100 43.88650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7195468E-02 0.1750330 midg,1,midg; midg,igrid,midg -0.4232870 -0.2990648 1,midg,midg; igrid,midg,midg 4.2252587E-03 0.1321079 gauss-seidel spectral radius is 0.9991704 estimated iterations to convergence 274 setup time was (sec) 1.590000 now iterating at: 23:53:44 rms-change max change #iterations 8.436928 343.5475 at 10iterations 4.728250 114.1549 at 20iterations 2.639499 59.53521 at 30iterations 1.472204 32.55642 at 40iterations 0.8178241 17.77313 at 50iterations 0.4555346 9.962780 at 60iterations 0.2539018 5.547489 at 70iterations 0.1408872 3.215410 at 80iterations 7.8375340E-02 1.751270 at 90iterations 4.3495834E-02 0.9319429 at 100iterations 2.4266860E-02 0.5059347 at 110iterations 1.3495116E-02 0.2990532 at 120iterations 7.5592156E-03 0.1561432 at 130iterations 4.2272480E-03 9.2077255E-02 at 140iterations 2.3840626E-03 4.9251556E-02 at 150iterations 1.3738764E-03 3.3290863E-02 at 160iterations 8.1200781E-04 2.0828247E-02 at 170iterations 4.9726537E-04 1.3481140E-02 at 180iterations finished qdiffx linear iterations at : 23:53:59 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 4.9726537E-04 1.3481140E-02 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.79000 DelPhi exited at 23:53:59 16.796u 0.473s 0:17.54 98.4% 0+0k 0+0io 0pf+0w