Sun Oct 9 19:33:51 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 Sun Oct 9 2011 at 19:33:51 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3011 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: 0.5434285 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 0.5434285 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 458.7693 centred at (gu) : 90.61961 89.61538 89.81447 assigned negative charge : -447.2704 centred at (gu) : 90.75353 89.63379 89.77204 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5802 nv = 96 ne = 84 npr = 59494 no. pairs analyzed = 59494 no. exposed pairs = 3798 no. arc points = 26909 no. surface atoms = 1279 nbur = 1732 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 = 1.568000 m= 236 mr = 2999 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 7609 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1246864E-10 8.7008895E-10 midg,1,midg; midg,igrid,midg 8.4085483E-10 4.9451460E-10 1,midg,midg; igrid,midg,midg 1.2479550E-09 -2.0865036E-10 gauss-seidel spectral radius is 0.9825468 estimated iterations to convergence 62 setup time was (sec) 0.7700000 now iterating at: 19:33:52 rms-change max change #iterations 6.9484584E-02 13.23973 at 10iterations 5.0119124E-03 0.8773270 at 20iterations 7.1573065E-04 0.1120415 at 30iterations 2.4418160E-04 3.7672043E-02 at 40iterations 9.5212163E-05 1.5039921E-02 at 50iterations finished qdiffx linear iterations at : 19:33:56 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 9.5212163E-05 1.5039921E-02 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 19:33:57 5.076u 0.453s 0:05.80 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 Sun Oct 9 2011 at 19:33:57 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3011 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: 1.630285 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 1.630285 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 458.7693 centred at (gu) : 91.85786 88.84531 89.44281 assigned negative charge : -447.2704 centred at (gu) : 92.26025 88.90116 89.31590 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26909 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20759 mr = 44479 m= 2261 mr = 14228 m= 76 mr = 1158 m= 0 mr = 1 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 372 time to turn everything in is 0.6800000 number of dielectric boundary points 28340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21968 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) : 0.5434285 object centre at (A) : 29.66600 10.93750 44.75200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2039431E-03 7.1692956E-03 midg,1,midg; midg,igrid,midg 9.3695177E-03 5.4880404E-03 1,midg,midg; igrid,midg,midg 2.2853257E-02 9.2062782E-03 gauss-seidel spectral radius is 0.9981821 estimated iterations to convergence 186 setup time was (sec) 1.030000 now iterating at: 19:33:59 rms-change max change #iterations 3.332870 157.7224 at 10iterations 1.388040 61.79839 at 20iterations 0.5800820 21.57161 at 30iterations 0.2414062 11.99094 at 40iterations 0.1009366 3.529761 at 50iterations 4.2084735E-02 1.681549 at 60iterations 1.7606495E-02 0.7493286 at 70iterations 7.4076988E-03 0.2711334 at 80iterations 3.1421862E-03 0.1107950 at 90iterations 1.3780294E-03 5.0205231E-02 at 100iterations 6.5509463E-04 2.5753021E-02 at 110iterations 3.5511190E-04 1.3613701E-02 at 120iterations finished qdiffx linear iterations at : 19:34:09 total time elapsed so far: 11.37000 # loops : 120 mean,max change (kT/e) : 3.5511190E-04 1.3613701E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 19:34:09 11.586u 0.506s 0:12.38 97.5% 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 Sun Oct 9 2011 at 19:34:09 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3011 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: 2.445428 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 2.445428 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 458.7693 centred at (gu) : 92.78677 88.26785 89.16395 assigned negative charge : -447.2704 centred at (gu) : 93.39041 88.35163 88.97381 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 150828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26909 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 71510 mr = 108663 m= 21318 mr = 56451 m= 3627 mr = 15914 m= 300 mr = 2369 m= 4 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1310 time to turn everything in is 1.690000 number of dielectric boundary points 64036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 22929 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) : 1.630285 object centre at (A) : 29.66600 10.93750 44.75200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4950059E-02 0.1012666 midg,1,midg; midg,igrid,midg 0.1411396 6.6337191E-02 1,midg,midg; igrid,midg,midg 0.3942626 0.2616802 gauss-seidel spectral radius is 0.9991371 estimated iterations to convergence 269 setup time was (sec) 2.070000 now iterating at: 19:34:12 rms-change max change #iterations 8.673956 281.3795 at 10iterations 4.901064 142.9624 at 20iterations 2.752290 70.48470 at 30iterations 1.537714 40.04610 at 40iterations 0.8568869 20.21970 at 50iterations 0.4751687 11.00560 at 60iterations 0.2634522 7.247467 at 70iterations 0.1458623 3.228670 at 80iterations 8.0480956E-02 1.921013 at 90iterations 4.4383395E-02 1.099921 at 100iterations 2.4518825E-02 0.5516129 at 110iterations 1.3547067E-02 0.2904694 at 120iterations 7.4750995E-03 0.1637421 at 130iterations 4.1242526E-03 8.8780403E-02 at 140iterations 2.2838423E-03 4.9687862E-02 at 150iterations 1.2698171E-03 2.5775909E-02 at 160iterations 7.1572291E-04 1.8768311E-02 at 170iterations 4.1311476E-04 9.3784332E-03 at 180iterations finished qdiffx linear iterations at : 19:34:29 total time elapsed so far: 19.42000 # loops : 180 mean,max change (kT/e) : 4.1311476E-04 9.3784332E-03 energy calculations done at 19.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.95000 DelPhi exited at 19:34:30 19.959u 0.519s 0:20.77 98.5% 0+0k 0+0io 0pf+0w