Mon Oct 10 13:59:08 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 13:59:08 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 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: 0.5350487 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 0.5350487 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 550.5858 centred at (gu) : 88.42920 89.77066 91.13930 assigned negative charge : -561.5876 centred at (gu) : 88.44006 89.80901 91.21368 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6750 nv = 96 ne = 84 npr = 78701 no. pairs analyzed = 78701 no. exposed pairs = 4282 no. arc points = 28797 no. surface atoms = 1467 nbur = 2251 mkacc time = 0.1900000 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 = 1.596000 m= 237 mr = 3756 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.4100000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2929 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8973 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7752394E-11 -1.1335229E-09 midg,1,midg; midg,igrid,midg -2.3930341E-10 -6.1324712E-10 1,midg,midg; igrid,midg,midg -5.5434829E-10 -3.3873676E-10 gauss-seidel spectral radius is 0.9820444 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 13:59:09 rms-change max change #iterations 7.4575230E-02 10.87622 at 10iterations 5.2939043E-03 0.8300438 at 20iterations 7.2911067E-04 0.1108828 at 30iterations 1.9682548E-04 3.4122467E-02 at 40iterations 5.8930673E-05 1.0398865E-02 at 50iterations finished qdiffx linear iterations at : 13:59:12 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 5.8930673E-05 1.0398865E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 13:59:13 3.686u 0.190s 0:04.34 89.1% 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 13:59:13 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 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: 1.605146 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 1.605146 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 550.5858 centred at (gu) : 85.28683 89.31112 93.41691 assigned negative charge : -561.5876 centred at (gu) : 85.31968 89.42653 93.64051 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 23433 mr = 54609 m= 2422 mr = 16484 m= 55 mr = 1281 m= 0 mr = 4 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1565 time to turn everything in is 0.5700000 number of dielectric boundary points 29755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 27126 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) : 0.5350487 object centre at (A) : 33.35800 15.25950 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2010580E-03 -2.7906246E-02 midg,1,midg; midg,igrid,midg -1.1562397E-02 -1.1981707E-02 1,midg,midg; igrid,midg,midg 1.1464109E-03 -6.0437829E-03 gauss-seidel spectral radius is 0.9981781 estimated iterations to convergence 186 setup time was (sec) 0.8900000 now iterating at: 13:59:14 rms-change max change #iterations 3.599873 159.4751 at 10iterations 1.499080 61.51436 at 20iterations 0.6238243 19.90579 at 30iterations 0.2611067 8.440780 at 40iterations 0.1086750 3.644453 at 50iterations 4.5512877E-02 1.480510 at 60iterations 1.9013338E-02 0.6184692 at 70iterations 8.0310078E-03 0.2584381 at 80iterations 3.4452593E-03 0.1156445 at 90iterations 1.5265848E-03 5.4649353E-02 at 100iterations 7.2598230E-04 2.7593404E-02 at 110iterations 3.8020132E-04 1.4396667E-02 at 120iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 3.8020132E-04 1.4396667E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 13:59:23 8.213u 0.236s 0:10.35 81.5% 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 Mon Oct 10 2011 at 13:59:23 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.407719 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 2.407719 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 550.5858 centred at (gu) : 82.92997 88.96642 95.12509 assigned negative charge : -561.5876 centred at (gu) : 82.97938 89.13963 95.46077 start vw surface at 0.2500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 177556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 82877 mr = 133239 m= 22657 mr = 66841 m= 3885 mr = 17206 m= 238 mr = 2690 m= 3 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 5435 time to turn everything in is 1.460000 number of dielectric boundary points 67127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 28415 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) : 1.605146 object centre at (A) : 33.35800 15.25950 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3528153 -0.4302782 midg,1,midg; midg,igrid,midg -0.1897610 -0.1682548 1,midg,midg; igrid,midg,midg 7.6411538E-02 -0.1901534 gauss-seidel spectral radius is 0.9991443 estimated iterations to convergence 270 setup time was (sec) 1.790000 now iterating at: 13:59:25 rms-change max change #iterations 9.436074 345.4326 at 10iterations 5.292218 127.7355 at 20iterations 2.960769 86.83257 at 30iterations 1.652027 35.79014 at 40iterations 0.9174915 18.74485 at 50iterations 0.5092450 10.27919 at 60iterations 0.2817874 5.340984 at 70iterations 0.1557760 3.066405 at 80iterations 8.5971683E-02 1.571701 at 90iterations 4.7502019E-02 0.9058914 at 100iterations 2.6257019E-02 0.4884553 at 110iterations 1.4530238E-02 0.2897606 at 120iterations 8.0556255E-03 0.1669006 at 130iterations 4.4831554E-03 8.3352573E-02 at 140iterations 2.5048475E-03 4.8612595E-02 at 150iterations 1.4310562E-03 2.7141571E-02 at 160iterations 8.3658379E-04 1.7994881E-02 at 170iterations 5.0668843E-04 1.0707855E-02 at 180iterations finished qdiffx linear iterations at : 13:59:37 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 5.0668843E-04 1.0707855E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 13:59:37 13.111u 0.241s 0:13.83 96.5% 0+0k 0+0io 0pf+0w