Sun Oct 9 02:43:35 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 Sun Oct 9 2011 at 02:43:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6350905 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): -16.64700 24.09800 ymin,ymax (A): 0.9090000 44.15300 zmin,zma (A): -19.36300 36.69200 x,y,z range (A): 40.74500 43.24400 56.05500 scale (grids/A): 0.6350905 object centre (A): 3.725500 22.53100 8.664501 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 90.38279 90.46002 90.61760 assigned negative charge : -326.4870 centred at (gu) : 90.39259 90.42629 90.63400 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5702 nv = 96 ne = 84 npr = 45944 no. pairs analyzed = 45944 no. exposed pairs = 2433 no. arc points = 16817 no. surface atoms = 838 nbur = 1328 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 266 mr = 3303 m= 0 mr = 34 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.2400000 number of dielectric boundary points 2631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1655 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2189573E-09 -7.3609860E-09 midg,1,midg; midg,igrid,midg -7.2162383E-09 -2.3713791E-09 1,midg,midg; igrid,midg,midg -3.8945456E-09 -6.3862458E-09 gauss-seidel spectral radius is 0.9871101 estimated iterations to convergence 72 setup time was (sec) 0.4800000 now iterating at: 02:43:36 rms-change max change #iterations 0.1274268 21.77237 at 10iterations 1.2497153E-02 1.739048 at 20iterations 1.1968013E-03 0.1959509 at 30iterations 1.1868343E-04 1.9476891E-02 at 40iterations 1.1481529E-05 1.8386841E-03 at 50iterations finished qdiffx linear iterations at : 02:43:38 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.1481529E-05 1.8386841E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 02:43:39 3.351u 0.223s 0:03.86 92.4% 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 02:43:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.905272 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): -16.64700 24.09800 ymin,ymax (A): 0.9090000 44.15300 zmin,zma (A): -19.36300 36.69200 x,y,z range (A): 40.74500 43.24400 56.05500 scale (grids/A): 1.905272 object centre (A): 3.725500 22.53100 8.664501 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 91.14803 91.37944 91.85275 assigned negative charge : -326.4870 centred at (gu) : 91.17781 91.27890 91.90201 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 21854 mr = 44401 m= 3336 mr = 16660 m= 185 mr = 2350 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3359 time to turn everything in is 0.4400000 number of dielectric boundary points 24085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 15974 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) : 0.6350905 object centre at (A) : 3.725500 22.53100 8.664501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4890835E-03 5.9796660E-04 midg,1,midg; midg,igrid,midg -4.4659884E-03 -1.2533988E-02 1,midg,midg; igrid,midg,midg -4.1954052E-03 -9.6343439E-03 gauss-seidel spectral radius is 0.9985787 estimated iterations to convergence 210 setup time was (sec) 0.7300000 now iterating at: 02:43:40 rms-change max change #iterations 3.836455 177.2045 at 10iterations 1.765603 66.13383 at 20iterations 0.8166108 27.84872 at 30iterations 0.3781604 14.58440 at 40iterations 0.1732906 5.370026 at 50iterations 8.0484696E-02 2.803909 at 60iterations 3.7232555E-02 1.233435 at 70iterations 1.7160296E-02 0.5894775 at 80iterations 7.9181194E-03 0.2739525 at 90iterations 3.6590358E-03 0.1345172 at 100iterations 1.6903653E-03 5.2141190E-02 at 110iterations 7.8032189E-04 2.7656555E-02 at 120iterations finished qdiffx linear iterations at : 02:43:47 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 7.8032189E-04 2.7656555E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 02:43:47 7.554u 0.263s 0:08.08 96.6% 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 Sun Oct 9 2011 at 02:43:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.857907 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): -16.64700 24.09800 ymin,ymax (A): 0.9090000 44.15300 zmin,zma (A): -19.36300 36.69200 x,y,z range (A): 40.74500 43.24400 56.05500 scale (grids/A): 2.857907 object centre (A): 3.725500 22.53100 8.664501 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 91.72205 92.06915 92.77912 assigned negative charge : -326.4870 centred at (gu) : 91.76677 91.91841 92.85311 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 144296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 71919 mr = 107488 m= 25371 mr = 60033 m= 6098 mr = 21050 m= 880 mr = 5025 m= 38 mr = 703 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 10997 time to turn everything in is 1.080000 number of dielectric boundary points 54295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 16262 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) : 1.905272 object centre at (A) : 3.725500 22.53100 8.664501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4163256 -0.1244271 midg,1,midg; midg,igrid,midg -5.4739818E-02 -0.1593600 1,midg,midg; igrid,midg,midg -6.2592752E-02 -7.7524982E-02 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 1.400000 now iterating at: 02:43:49 rms-change max change #iterations 8.817863 415.4547 at 10iterations 4.997005 108.0214 at 20iterations 2.831801 64.11938 at 30iterations 1.604591 31.42749 at 40iterations 0.9054492 18.21666 at 50iterations 0.5127758 10.11103 at 60iterations 0.2891876 5.682262 at 70iterations 0.1636173 3.170850 at 80iterations 9.2545435E-02 1.694463 at 90iterations 5.2461479E-02 0.9542999 at 100iterations 2.9695973E-02 0.6534519 at 110iterations 1.6778490E-02 0.3363113 at 120iterations 9.5317317E-03 0.1761208 at 130iterations 5.3800270E-03 0.1122580 at 140iterations 3.0439068E-03 5.8446884E-02 at 150iterations 1.7242517E-03 3.3695221E-02 at 160iterations 9.7519660E-04 1.8152237E-02 at 170iterations 5.5234443E-04 9.9220276E-03 at 180iterations finished qdiffx linear iterations at : 02:44:01 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 5.5234443E-04 9.9220276E-03 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.99000 DelPhi exited at 02:44:02 13.992u 0.266s 0:14.53 98.0% 0+0k 0+0io 0pf+0w