Sat Oct 15 13:58:16 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 Sat Oct 15 2011 at 13:58:20 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5136122 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): -16.08500 36.45400 ymin,ymax (A): -32.14800 31.34000 zmin,zma (A): -3.801000 65.51200 x,y,z range (A): 52.53900 63.48800 69.31300 scale (grids/A): 0.5136122 object centre (A): 10.18450 -0.4039993 30.85550 number of atom coordinates read : 4295 total number of charged atoms : 4093 net assigned charge : -9.9968195E-02 assigned positive charge : 642.4583 centred at (gu) : 90.39545 90.65407 87.68639 assigned negative charge : -642.5623 centred at (gu) : 90.27386 90.72697 87.80613 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7120 nv = 96 ne = 84 npr = 87767 no. pairs analyzed = 87767 no. exposed pairs = 5507 no. arc points = 38083 no. surface atoms = 1852 nbur = 2443 mkacc time = 0.2400000 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 = 1.652000 m= 264 mr = 3647 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3660 ## 511 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6227439E-10 -1.7967526E-10 midg,1,midg; midg,igrid,midg 1.5203810E-10 -2.4213911E-10 1,midg,midg; igrid,midg,midg -3.0153424E-10 3.3984215E-10 gauss-seidel spectral radius is 0.9805780 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 13:58:25 rms-change max change #iterations 6.7466989E-02 9.749077 at 10iterations 3.8699266E-03 0.6486645 at 20iterations 2.6995596E-04 4.5681000E-02 at 30iterations 5.5419128E-05 9.6259117E-03 at 40iterations 1.9394904E-05 3.4035444E-03 at 50iterations finished qdiffx linear iterations at : 13:58:35 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.9394904E-05 3.4035444E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 13:58:36 4.236u 0.264s 0:16.92 26.5% 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 Sat Oct 15 2011 at 13:58:38 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.540836 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): -16.08500 36.45400 ymin,ymax (A): -32.14800 31.34000 zmin,zma (A): -3.801000 65.51200 x,y,z range (A): 52.53900 63.48800 69.31300 scale (grids/A): 1.540836 object centre (A): 10.18450 -0.4039993 30.85550 number of atom coordinates read : 4295 total number of charged atoms : 4093 net assigned charge : -9.9968195E-02 assigned positive charge : 642.4583 centred at (gu) : 91.18504 91.96098 83.05782 assigned negative charge : -642.5623 centred at (gu) : 90.82122 92.18042 83.41822 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38083 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23095 mr = 54705 m= 2027 mr = 15153 m= 43 mr = 863 m= 0 mr = 2 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.7300000 number of dielectric boundary points 34776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 460 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 30826 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) : 0.5136122 object centre at (A) : 10.18450 -0.4039993 30.85550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4043584E-03 -1.4446204E-02 midg,1,midg; midg,igrid,midg -9.3559775E-04 -1.1528235E-02 1,midg,midg; igrid,midg,midg -3.2610192E-03 9.1258371E-03 gauss-seidel spectral radius is 0.9980888 estimated iterations to convergence 182 setup time was (sec) 1.040000 now iterating at: 13:58:44 rms-change max change #iterations 3.603080 156.2364 at 10iterations 1.460482 49.49622 at 20iterations 0.5972924 21.06324 at 30iterations 0.2426152 9.296546 at 40iterations 9.8856241E-02 3.224937 at 50iterations 4.0381040E-02 1.500425 at 60iterations 1.6434480E-02 0.5405479 at 70iterations 6.7260023E-03 0.2201943 at 80iterations 2.7634436E-03 9.8896742E-02 at 90iterations 1.1478438E-03 3.7540436E-02 at 100iterations 4.8338668E-04 1.6754627E-02 at 110iterations 2.1620172E-04 6.7729950E-03 at 120iterations finished qdiffx linear iterations at : 13:59:10 total time elapsed so far: 9.680000 # loops : 120 mean,max change (kT/e) : 2.1620172E-04 6.7729950E-03 energy calculations done at 9.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 13:59:12 9.861u 0.283s 0:33.61 30.1% 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 Sat Oct 15 2011 at 13:59:18 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.311255 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): -16.08500 36.45400 ymin,ymax (A): -32.14800 31.34000 zmin,zma (A): -3.801000 65.51200 x,y,z range (A): 52.53900 63.48800 69.31300 scale (grids/A): 2.311255 object centre (A): 10.18450 -0.4039993 30.85550 number of atom coordinates read : 4295 total number of charged atoms : 4093 net assigned charge : -9.9968195E-02 assigned positive charge : 642.4583 centred at (gu) : 91.77715 92.94118 79.58633 assigned negative charge : -642.5623 centred at (gu) : 91.23178 93.27061 80.12727 start vw surface at 0.2200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 187206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38083 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 82582 mr = 134565 m= 20935 mr = 64182 m= 3064 mr = 14748 m= 181 mr = 1862 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 518 time to turn everything in is 1.780000 number of dielectric boundary points 78548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 32663 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) : 1.540836 object centre at (A) : 10.18450 -0.4039993 30.85550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1387661 -0.3095995 midg,1,midg; midg,igrid,midg -7.7266939E-02 -0.2533711 1,midg,midg; igrid,midg,midg -4.4436499E-02 0.1279252 gauss-seidel spectral radius is 0.9991441 estimated iterations to convergence 270 setup time was (sec) 2.130000 now iterating at: 13:59:27 rms-change max change #iterations 9.782798 303.9681 at 10iterations 5.552891 156.5807 at 20iterations 3.139798 65.85967 at 30iterations 1.767295 40.87782 at 40iterations 0.9894834 20.94299 at 50iterations 0.5525360 12.86590 at 60iterations 0.3074913 7.511319 at 70iterations 0.1706020 3.624396 at 80iterations 9.4634138E-02 1.863056 at 90iterations 5.2562088E-02 1.059994 at 100iterations 2.9076489E-02 0.6534548 at 110iterations 1.6088052E-02 0.3554096 at 120iterations 8.8813035E-03 0.1707268 at 130iterations 4.9055791E-03 9.3700409E-02 at 140iterations 2.7203911E-03 5.6621552E-02 at 150iterations 1.5038942E-03 3.1133652E-02 at 160iterations 8.3256164E-04 1.6353369E-02 at 170iterations 4.6194106E-04 9.6836090E-03 at 180iterations finished qdiffx linear iterations at : 14:00:12 total time elapsed so far: 16.63000 # loops : 180 mean,max change (kT/e) : 4.6194106E-04 9.6836090E-03 energy calculations done at 16.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 14:00:13 16.816u 0.312s 0:56.08 30.5% 0+0k 0+0io 0pf+0w