Sun Oct 9 15:07:47 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 15:07:47 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 = 5728 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 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: 0.5085859 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 0.5085859 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.971960 assigned positive charge : 879.6473 centred at (gu) : 89.90628 88.86066 88.30749 assigned negative charge : -886.6270 centred at (gu) : 89.95744 88.96246 88.24930 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9049 nv = 96 ne = 84 npr = 118863 no. pairs analyzed = 118863 no. exposed pairs = 6510 no. arc points = 45254 no. surface atoms = 2206 nbur = 3522 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 = 1.680000 m= 318 mr = 5039 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3700000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4334 ## 643 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1336876E-10 4.9359291E-11 midg,1,midg; midg,igrid,midg 2.7999644E-10 -2.9143374E-10 1,midg,midg; igrid,midg,midg 6.0415631E-11 -2.3600910E-10 gauss-seidel spectral radius is 0.9802806 estimated iterations to convergence 59 setup time was (sec) 0.5600000 now iterating at: 15:07:47 rms-change max change #iterations 7.4103422E-02 9.934265 at 10iterations 4.5159692E-03 0.6392193 at 20iterations 5.2276568E-04 7.2187424E-02 at 30iterations 1.3311321E-04 1.9203186E-02 at 40iterations 4.0802872E-05 5.3777695E-03 at 50iterations finished qdiffx linear iterations at : 15:07:50 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.0802872E-05 5.3777695E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:07:51 3.555u 0.177s 0:04.00 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 Sun Oct 9 2011 at 15:07:51 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 = 5728 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 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: 1.525758 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 1.525758 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.971960 assigned positive charge : 879.6473 centred at (gu) : 89.71702 86.58011 84.92095 assigned negative charge : -886.6270 centred at (gu) : 89.87229 86.88694 84.74761 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45254 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29885 mr = 74452 m= 2639 mr = 20673 m= 62 mr = 1140 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3538 time to turn everything in is 0.5000000 number of dielectric boundary points 40437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 613 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 41674 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) : 0.5085859 object centre at (A) : 18.60700 130.3145 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2713170E-03 -8.1327959E-04 midg,1,midg; midg,igrid,midg 6.2163570E-03 -2.0714359E-02 1,midg,midg; igrid,midg,midg -2.1899039E-02 -1.4226718E-02 gauss-seidel spectral radius is 0.9981576 estimated iterations to convergence 185 setup time was (sec) 0.7200000 now iterating at: 15:07:52 rms-change max change #iterations 4.247169 145.9132 at 10iterations 1.761974 53.53476 at 20iterations 0.7319638 21.94105 at 30iterations 0.3040261 9.396861 at 40iterations 0.1260134 3.889889 at 50iterations 5.2528236E-02 1.594384 at 60iterations 2.1882186E-02 0.6591573 at 70iterations 9.0565132E-03 0.2570572 at 80iterations 3.7821799E-03 0.1145020 at 90iterations 1.5864051E-03 4.6058655E-02 at 100iterations 6.6794507E-04 1.9549370E-02 at 110iterations 2.8687401E-04 8.4533691E-03 at 120iterations finished qdiffx linear iterations at : 15:07:59 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.8687401E-04 8.4533691E-03 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 15:07:59 7.934u 0.193s 0:08.45 96.0% 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 Sun Oct 9 2011 at 15:07:59 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 = 5728 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 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: 2.288637 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 2.288637 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.971960 assigned positive charge : 879.6473 centred at (gu) : 89.57491 84.86972 82.38087 assigned negative charge : -886.6270 centred at (gu) : 89.80827 85.33022 82.12129 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45254 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108977 mr = 182505 m= 27127 mr = 87115 m= 3786 mr = 20232 m= 189 mr = 2323 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 11519 time to turn everything in is 1.190000 number of dielectric boundary points 91219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 44307 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) : 1.525758 object centre at (A) : 18.60700 130.3145 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2628635E-02 -8.9245841E-02 midg,1,midg; midg,igrid,midg 8.3169512E-02 -0.4409964 1,midg,midg; igrid,midg,midg -0.3024284 -0.1663392 gauss-seidel spectral radius is 0.9991814 estimated iterations to convergence 276 setup time was (sec) 1.440000 now iterating at: 15:08:01 rms-change max change #iterations 11.38503 297.1486 at 10iterations 6.532330 146.0213 at 20iterations 3.715844 85.82753 at 30iterations 2.105511 45.69060 at 40iterations 1.189592 24.04764 at 50iterations 0.6699430 13.25900 at 60iterations 0.3774608 6.780294 at 70iterations 0.2122945 3.663206 at 80iterations 0.1189462 2.072159 at 90iterations 6.6772483E-02 1.178695 at 100iterations 3.7400566E-02 0.7022438 at 110iterations 2.0990275E-02 0.3366604 at 120iterations 1.1726421E-02 0.1982155 at 130iterations 6.5835677E-03 0.1057634 at 140iterations 3.6793062E-03 6.7153931E-02 at 150iterations 2.0589847E-03 3.3573151E-02 at 160iterations 1.1581643E-03 1.9535065E-02 at 170iterations 6.5008289E-04 1.1070251E-02 at 180iterations finished qdiffx linear iterations at : 15:08:12 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 6.5008289E-04 1.1070251E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 15:08:13 13.183u 0.215s 0:13.67 97.9% 0+0k 0+0io 0pf+0w