Sat Oct 15 14:00:22 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 Sat Oct 15 2011 at 14:00:24 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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= 0.1200000 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 : 4089 net assigned charge : -0.1939719 assigned positive charge : 642.0983 centred at (gu) : 90.40021 90.65501 87.68705 assigned negative charge : -642.2963 centred at (gu) : 90.27802 90.72746 87.80694 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 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 = 0.2500000 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 = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 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 0.6400000 number of grid points assigned charge 9557 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5979971E-10 -1.8071432E-10 midg,1,midg; midg,igrid,midg 1.4962966E-10 -2.4246816E-10 1,midg,midg; igrid,midg,midg -3.0390615E-10 3.4012607E-10 gauss-seidel spectral radius is 0.9805780 estimated iterations to convergence 59 setup time was (sec) 0.7900000 now iterating at: 14:00:28 rms-change max change #iterations 6.7596115E-02 9.819044 at 10iterations 3.8738404E-03 0.6454830 at 20iterations 2.6236847E-04 4.4422150E-02 at 30iterations 5.0002669E-05 8.6967945E-03 at 40iterations 1.7325567E-05 3.0583739E-03 at 50iterations finished qdiffx linear iterations at : 14:00:38 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.7325567E-05 3.0583739E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 14:00:39 4.347u 0.292s 0:15.52 29.8% 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 14:00:41 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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= 0.1200000 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 : 4089 net assigned charge : -0.1939719 assigned positive charge : 642.0983 centred at (gu) : 91.19933 91.96384 83.05981 assigned negative charge : -642.2963 centred at (gu) : 90.83369 92.18188 83.42069 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 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 0.7400000 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 0.8800000 number of grid points assigned charge 30798 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 3.3575860E-03 -1.4470501E-02 midg,1,midg; midg,igrid,midg -9.9181570E-04 -1.1562862E-02 1,midg,midg; igrid,midg,midg -3.3643041E-03 9.0988027E-03 gauss-seidel spectral radius is 0.9980888 estimated iterations to convergence 182 setup time was (sec) 1.050000 now iterating at: 14:00:48 rms-change max change #iterations 3.603976 156.2364 at 10iterations 1.460582 49.49623 at 20iterations 0.5973688 21.03654 at 30iterations 0.2426566 9.346959 at 40iterations 9.8887324E-02 3.210758 at 50iterations 4.0391058E-02 1.481802 at 60iterations 1.6439520E-02 0.5448101 at 70iterations 6.7254882E-03 0.2223830 at 80iterations 2.7615966E-03 9.7682953E-02 at 90iterations 1.1451673E-03 3.6800385E-02 at 100iterations 4.8021160E-04 1.6407013E-02 at 110iterations 2.1273619E-04 6.7424774E-03 at 120iterations finished qdiffx linear iterations at : 14:01:14 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 2.1273619E-04 6.7424774E-03 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 14:01:16 9.856u 0.313s 0:34.69 29.2% 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 14:01:16 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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 : 4089 net assigned charge : -0.1939719 assigned positive charge : 642.0983 centred at (gu) : 91.79858 92.94547 79.58930 assigned negative charge : -642.2963 centred at (gu) : 91.25048 93.27280 80.13097 start vw surface at 0.2000000 fill in re-entrant regions at 0.6000000 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 1.770000 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 1.930000 number of grid points assigned charge 32631 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 0.1378854 -0.3099651 midg,1,midg; midg,igrid,midg -7.8091606E-02 -0.2539610 1,midg,midg; igrid,midg,midg -4.6268560E-02 0.1273263 gauss-seidel spectral radius is 0.9991441 estimated iterations to convergence 270 setup time was (sec) 2.120000 now iterating at: 14:01:23 rms-change max change #iterations 9.784210 303.9681 at 10iterations 5.554145 156.5802 at 20iterations 3.140402 66.92227 at 30iterations 1.767553 41.14075 at 40iterations 0.9896084 20.90829 at 50iterations 0.5526040 12.77905 at 60iterations 0.3075541 7.554058 at 70iterations 0.1706350 3.607706 at 80iterations 9.4643481E-02 1.857944 at 90iterations 5.2569017E-02 1.050023 at 100iterations 2.9082805E-02 0.6493783 at 110iterations 1.6089655E-02 0.3547344 at 120iterations 8.8830041E-03 0.1715164 at 130iterations 4.9058627E-03 9.4678879E-02 at 140iterations 2.7201003E-03 5.6785583E-02 at 150iterations 1.5033208E-03 3.1434059E-02 at 160iterations 8.3179172E-04 1.6363621E-02 at 170iterations 4.6099909E-04 9.6874237E-03 at 180iterations finished qdiffx linear iterations at : 14:02:00 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 4.6099909E-04 9.6874237E-03 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.80000 DelPhi exited at 14:02:02 16.802u 0.386s 0:46.06 37.2% 0+0k 0+0io 0pf+0w