Sat Oct 15 12:57:17 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 12:57:17 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 171 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7125273 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 0.7125273 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2138 net assigned charge : 5.326011 assigned positive charge : 348.1913 centred at (gu) : 90.36196 90.53015 90.41100 assigned negative charge : -342.8657 centred at (gu) : 90.41071 90.58752 90.50182 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8065 nv = 96 ne = 84 npr = 45476 no. pairs analyzed = 45476 no. exposed pairs = 2815 no. arc points = 20046 no. surface atoms = 950 nbur = 1336 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 546 mr = 4556 m= 6 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1910 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8728 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7922218E-08 -5.1217444E-09 midg,1,midg; midg,igrid,midg 7.7668105E-08 1.7607572E-08 1,midg,midg; igrid,midg,midg 7.5367460E-08 2.2830319E-08 gauss-seidel spectral radius is 0.9897584 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 12:57:18 rms-change max change #iterations 0.2188208 25.97266 at 10iterations 2.8074769E-02 3.370717 at 20iterations 3.9262557E-03 0.5769882 at 30iterations 8.2693773E-04 0.1290398 at 40iterations 2.6923403E-04 4.2934418E-02 at 50iterations finished qdiffx linear iterations at : 12:57:21 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.6923403E-04 4.2934418E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 12:57:22 3.504u 0.217s 0:04.11 90.2% 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 12:57:22 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 171 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.137582 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 2.137582 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2138 net assigned charge : 5.326011 assigned positive charge : 348.1913 centred at (gu) : 91.08546 91.59012 91.23266 assigned negative charge : -342.8657 centred at (gu) : 91.23179 91.76241 91.50538 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 85409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20046 grid for indexing accessible points = 1.400000 m= 34150 mr = 59951 m= 6830 mr = 25960 m= 660 mr = 4580 m= 19 mr = 332 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 36243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17015 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) : 0.7125273 object centre at (A) : 5.208500 4.067500 24.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8759069E-02 7.5201695E-03 midg,1,midg; midg,igrid,midg -5.4136463E-03 -7.1192548E-02 1,midg,midg; igrid,midg,midg -1.1084575E-02 7.4575905E-04 gauss-seidel spectral radius is 0.9988764 estimated iterations to convergence 236 setup time was (sec) 0.6500000 now iterating at: 12:57:22 rms-change max change #iterations 5.000452 241.7747 at 10iterations 2.494851 76.94183 at 20iterations 1.253935 39.74707 at 30iterations 0.6291000 19.54250 at 40iterations 0.3177490 8.869562 at 50iterations 0.1597880 5.825098 at 60iterations 8.0465294E-02 2.186979 at 70iterations 4.0666088E-02 1.374384 at 80iterations 2.0561188E-02 0.5990067 at 90iterations 1.0491646E-02 0.3073692 at 100iterations 5.4218671E-03 0.1622505 at 110iterations 2.8726936E-03 9.4490051E-02 at 120iterations finished qdiffx linear iterations at : 12:57:34 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 2.8726936E-03 9.4490051E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 12:57:34 8.198u 0.223s 0:12.44 67.6% 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 12:57:34 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 171 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.206373 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 3.206373 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2138 net assigned charge : 5.326011 assigned positive charge : 348.1913 centred at (gu) : 91.62823 92.38508 91.84893 assigned negative charge : -342.8657 centred at (gu) : 91.84758 92.64359 92.25806 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 196577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20046 grid for indexing accessible points = 1.400000 m= 106305 mr = 144157 m= 43696 mr = 88466 m= 12996 mr = 35741 m= 2682 mr = 10224 m= 318 mr = 1986 m= 22 mr = 197 m= 0 mr = 11 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 81814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17103 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) : 2.137582 object centre at (A) : 5.208500 4.067500 24.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5669138 -5.5154555E-02 midg,1,midg; midg,igrid,midg -0.4899436 -0.9766837 1,midg,midg; igrid,midg,midg -0.2849311 -0.1617040 gauss-seidel spectral radius is 0.9993114 estimated iterations to convergence 301 setup time was (sec) 1.560000 now iterating at: 12:57:36 rms-change max change #iterations 11.09092 404.0645 at 10iterations 6.617380 153.1036 at 20iterations 3.925334 74.39075 at 30iterations 2.332433 45.79474 at 40iterations 1.377583 24.72585 at 50iterations 0.8156212 13.80145 at 60iterations 0.4813050 8.203066 at 70iterations 0.2833599 5.119328 at 80iterations 0.1670204 2.889914 at 90iterations 9.8540023E-02 1.749687 at 100iterations 5.8171127E-02 0.9480631 at 110iterations 3.4495562E-02 0.5807648 at 120iterations 2.0616654E-02 0.3623276 at 130iterations 1.2549352E-02 0.2202978 at 140iterations 7.8619421E-03 0.1477737 at 150iterations 5.1712994E-03 0.1077595 at 160iterations 3.6144003E-03 7.5798035E-02 at 170iterations 2.6965244E-03 5.6766510E-02 at 180iterations finished qdiffx linear iterations at : 12:57:50 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 2.6965244E-03 5.6766510E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 12:57:51 13.721u 0.238s 0:16.54 84.3% 0+0k 0+0io 0pf+0w