Sat Oct 8 15:48:29 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 8 2011 at 15:48:30 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6555445 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 0.6555445 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.400002 assigned positive charge : 360.2549 centred at (gu) : 90.24435 88.81010 90.48700 assigned negative charge : -355.8557 centred at (gu) : 90.19880 88.97899 90.54272 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6960 nv = 96 ne = 84 npr = 49908 no. pairs analyzed = 49908 no. exposed pairs = 3011 no. arc points = 21039 no. surface atoms = 1040 nbur = 1396 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3837 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2800000 number of dielectric boundary points 3508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6759989E-08 5.2439353E-10 midg,1,midg; midg,igrid,midg 4.6821768E-08 -1.4025558E-08 1,midg,midg; igrid,midg,midg 2.1059783E-09 1.7788546E-08 gauss-seidel spectral radius is 0.9879261 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 15:48:30 rms-change max change #iterations 0.1537925 21.28981 at 10iterations 1.6432427E-02 2.299751 at 20iterations 1.7432718E-03 0.2407837 at 30iterations 2.1812542E-04 3.1380653E-02 at 40iterations 4.1357358E-05 5.4979324E-03 at 50iterations finished qdiffx linear iterations at : 15:48:34 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 4.1357358E-05 5.4979324E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 15:48:35 4.423u 0.406s 0:05.09 94.6% 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 8 2011 at 15:48:35 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 1.966634 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 1.966634 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.400002 assigned positive charge : 360.2549 centred at (gu) : 90.73256 86.42976 91.46046 assigned negative charge : -355.8557 centred at (gu) : 90.59625 86.93690 91.62790 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21039 grid for indexing accessible points = 1.400000 m= 29029 mr = 51468 m= 5891 mr = 21702 m= 448 mr = 4037 m= 11 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1067 time to turn everything in is 0.6200000 number of dielectric boundary points 32100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18436 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) : 0.6555445 object centre at (A) : 48.59400 39.87550 9.063000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0125177E-02 -2.0205382E-02 midg,1,midg; midg,igrid,midg 3.5911892E-02 -6.2185102E-03 1,midg,midg; igrid,midg,midg 7.7052996E-03 -1.3299489E-03 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 0.9200000 now iterating at: 15:48:36 rms-change max change #iterations 4.323728 182.8712 at 10iterations 2.055372 77.94759 at 20iterations 0.9797529 30.62225 at 30iterations 0.4659852 13.95111 at 40iterations 0.2221157 7.370008 at 50iterations 0.1058383 3.451340 at 60iterations 5.0669465E-02 1.500683 at 70iterations 2.4181427E-02 0.7739296 at 80iterations 1.1540622E-02 0.3725946 at 90iterations 5.5271410E-03 0.1662753 at 100iterations 2.6522358E-03 8.5777283E-02 at 110iterations 1.2733708E-03 4.0721893E-02 at 120iterations finished qdiffx linear iterations at : 15:48:46 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 1.2733708E-03 4.0721893E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 15:48:46 10.680u 0.453s 0:11.41 97.5% 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 Sat Oct 8 2011 at 15:48:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.949950 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 2.949950 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.400002 assigned positive charge : 360.2549 centred at (gu) : 91.09871 84.64439 92.19034 assigned negative charge : -355.8557 centred at (gu) : 90.89431 85.40524 92.44176 start vw surface at 0.1000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 171130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21039 grid for indexing accessible points = 1.400000 m= 89829 mr = 124611 m= 37605 mr = 73787 m= 11207 mr = 30906 m= 2001 mr = 8822 m= 190 mr = 1377 m= 4 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 3623 time to turn everything in is 1.670000 number of dielectric boundary points 72378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 18676 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) : 1.966634 object centre at (A) : 48.59400 39.87550 9.063000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2125874 -0.2495099 midg,1,midg; midg,igrid,midg 0.2465256 -8.6161271E-02 1,midg,midg; igrid,midg,midg 9.5433928E-02 -0.1257552 gauss-seidel spectral radius is 0.9992732 estimated iterations to convergence 293 setup time was (sec) 2.010000 now iterating at: 15:48:49 rms-change max change #iterations 10.10101 369.4139 at 10iterations 5.938185 177.2556 at 20iterations 3.481226 79.34161 at 30iterations 2.038127 42.16385 at 40iterations 1.188669 24.69659 at 50iterations 0.6913560 12.44764 at 60iterations 0.4015910 7.786930 at 70iterations 0.2332794 4.413445 at 80iterations 0.1352519 2.301210 at 90iterations 7.8329600E-02 1.351527 at 100iterations 4.5423973E-02 0.8428345 at 110iterations 2.6235892E-02 0.4791818 at 120iterations 1.5190688E-02 0.2643831 at 130iterations 8.8047888E-03 0.1557388 at 140iterations 5.1180804E-03 8.2769394E-02 at 150iterations 2.9666221E-03 5.4569244E-02 at 160iterations 1.7367131E-03 3.2179832E-02 at 170iterations 1.0239844E-03 1.8341064E-02 at 180iterations finished qdiffx linear iterations at : 15:49:05 total time elapsed so far: 17.96000 # loops : 180 mean,max change (kT/e) : 1.0239844E-03 1.8341064E-02 energy calculations done at 17.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.13000 DelPhi exited at 15:49:05 18.130u 0.481s 0:18.89 98.5% 0+0k 0+0io 0pf+0w