Tue Oct 11 03:48:10 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 Tue Oct 11 2011 at 03:48:10 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 = 2754 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: 0.6622517 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 0.6622517 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2606 net assigned charge : 3.500013 assigned positive charge : 417.6396 centred at (gu) : 89.45958 90.34724 91.30772 assigned negative charge : -414.1403 centred at (gu) : 89.18174 90.20606 91.29739 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8133 nv = 96 ne = 84 npr = 55842 no. pairs analyzed = 55842 no. exposed pairs = 3301 no. arc points = 22888 no. surface atoms = 1102 nbur = 1652 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4725 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2100000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2240 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7854517E-09 1.5775207E-08 midg,1,midg; midg,igrid,midg -2.0593371E-08 4.3890157E-08 1,midg,midg; igrid,midg,midg -6.0749848E-08 6.2508320E-08 gauss-seidel spectral radius is 0.9881921 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 03:48:11 rms-change max change #iterations 0.1751113 25.54650 at 10iterations 1.9312957E-02 2.567556 at 20iterations 2.0710086E-03 0.2651596 at 30iterations 2.4954276E-04 3.1581879E-02 at 40iterations 4.0613642E-05 6.7119598E-03 at 50iterations finished qdiffx linear iterations at : 03:48:14 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.0613642E-05 6.7119598E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:48:15 3.382u 0.157s 0:04.18 84.4% 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 Tue Oct 11 2011 at 03:48:15 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 = 2754 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: 1.986755 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 1.986755 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2606 net assigned charge : 3.500013 assigned positive charge : 417.6396 centred at (gu) : 88.37839 91.04114 93.92284 assigned negative charge : -414.1403 centred at (gu) : 87.54474 90.61772 93.89194 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 87048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 33799 mr = 62212 m= 5948 mr = 25804 m= 431 mr = 4050 m= 6 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 0.4000000 number of dielectric boundary points 34942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20583 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) : 0.6622517 object centre at (A) : 13.50700 -2.318000 18.76100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5967770E-03 1.0258247E-02 midg,1,midg; midg,igrid,midg -1.7797304E-02 8.7434631E-03 1,midg,midg; igrid,midg,midg -2.8530067E-02 6.4296484E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 0.6100000 now iterating at: 03:48:15 rms-change max change #iterations 4.787508 231.5635 at 10iterations 2.318473 73.08298 at 20iterations 1.129153 33.55644 at 30iterations 0.5455363 15.48147 at 40iterations 0.2658116 7.594267 at 50iterations 0.1288634 3.860806 at 60iterations 6.2693201E-02 2.010080 at 70iterations 3.0341368E-02 0.8803916 at 80iterations 1.4776780E-02 0.4175558 at 90iterations 7.1698111E-03 0.1975141 at 100iterations 3.4828342E-03 0.1010303 at 110iterations 1.6983812E-03 4.7945023E-02 at 120iterations finished qdiffx linear iterations at : 03:48:22 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.6983812E-03 4.7945023E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 03:48:23 7.746u 0.224s 0:08.45 94.2% 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 Tue Oct 11 2011 at 03:48:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 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: 2.980132 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 2.980132 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2606 net assigned charge : 3.500013 assigned positive charge : 417.6396 centred at (gu) : 87.56747 91.56169 95.88395 assigned negative charge : -414.1403 centred at (gu) : 86.31701 90.92645 95.83763 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 107256 mr = 149748 m= 41596 mr = 89676 m= 11101 mr = 34428 m= 1885 mr = 8792 m= 165 mr = 1443 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1363 time to turn everything in is 1.110000 number of dielectric boundary points 78924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20840 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) : 1.986755 object centre at (A) : 13.50700 -2.318000 18.76100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0960722E-02 0.2894915 midg,1,midg; midg,igrid,midg -0.2094642 6.0666665E-02 1,midg,midg; igrid,midg,midg -0.2264762 0.5369180 gauss-seidel spectral radius is 0.9992852 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 03:48:25 rms-change max change #iterations 10.95541 376.5963 at 10iterations 6.433379 146.7535 at 20iterations 3.770629 75.75266 at 30iterations 2.204244 45.09956 at 40iterations 1.289925 24.52671 at 50iterations 0.7534477 13.68446 at 60iterations 0.4391693 7.418566 at 70iterations 0.2562900 4.607674 at 80iterations 0.1491793 2.855406 at 90iterations 8.6847953E-02 1.415243 at 100iterations 5.0448302E-02 0.8617153 at 110iterations 2.9309945E-02 0.4868774 at 120iterations 1.7041750E-02 0.2856445 at 130iterations 9.9298824E-03 0.1634827 at 140iterations 5.7695354E-03 9.5142365E-02 at 150iterations 3.3620500E-03 6.1035156E-02 at 160iterations 1.9640171E-03 3.3584595E-02 at 170iterations 1.1583104E-03 2.0568848E-02 at 180iterations finished qdiffx linear iterations at : 03:48:36 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.1583104E-03 2.0568848E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 03:48:37 12.730u 0.208s 0:13.42 96.3% 0+0k 0+0io 0pf+0w