Sat Oct 8 16:20:35 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 Sat Oct 8 2011 at 16:20:36 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 = 2355 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: 0.5854493 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 0.5854493 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2266 net assigned charge : 4.000001 assigned positive charge : 348.1421 centred at (gu) : 90.26624 88.84975 88.78385 assigned negative charge : -344.1427 centred at (gu) : 90.31159 88.97160 88.81261 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5244 nv = 96 ne = 84 npr = 48440 no. pairs analyzed = 48440 no. exposed pairs = 2942 no. arc points = 20369 no. surface atoms = 1004 nbur = 1351 mkacc time = 0.1300000 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 = 1.456000 m= 207 mr = 2760 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2111 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1163129E-09 3.3403144E-10 midg,1,midg; midg,igrid,midg 4.5291282E-09 -1.1319385E-09 1,midg,midg; igrid,midg,midg 1.8189590E-09 9.1208818E-11 gauss-seidel spectral radius is 0.9848846 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 16:20:36 rms-change max change #iterations 8.8301986E-02 19.27292 at 10iterations 7.0160409E-03 1.079844 at 20iterations 5.9383898E-04 9.2943192E-02 at 30iterations 6.7345551E-05 1.3389587E-02 at 40iterations 1.3338487E-05 2.9625893E-03 at 50iterations finished qdiffx linear iterations at : 16:20:40 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.3338487E-05 2.9625893E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 16:20:41 4.474u 0.361s 0:05.13 94.1% 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 16:20:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 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: 1.756348 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 1.756348 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2266 net assigned charge : 4.000001 assigned positive charge : 348.1421 centred at (gu) : 90.79845 86.54900 86.35094 assigned negative charge : -344.1427 centred at (gu) : 90.93462 86.91485 86.43771 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20369 grid for indexing accessible points = 1.400000 m= 18495 mr = 39301 m= 2341 mr = 13064 m= 81 mr = 1369 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 24670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 17633 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) : 0.5854493 object centre at (A) : 22.03000 6.888500 11.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6757997E-02 1.3660823E-02 midg,1,midg; midg,igrid,midg 1.3092220E-02 -1.7674912E-03 1,midg,midg; igrid,midg,midg 5.1163258E-03 -1.6326381E-02 gauss-seidel spectral radius is 0.9983679 estimated iterations to convergence 196 setup time was (sec) 0.8000000 now iterating at: 16:20:42 rms-change max change #iterations 3.371702 174.4995 at 10iterations 1.477013 55.76887 at 20iterations 0.6453185 25.11342 at 30iterations 0.2824129 10.65165 at 40iterations 0.1235255 4.573988 at 50iterations 5.3880721E-02 1.934090 at 60iterations 2.3473877E-02 0.8176537 at 70iterations 1.0269831E-02 0.3666801 at 80iterations 4.4969148E-03 0.1842003 at 90iterations 1.9671011E-03 7.4251175E-02 at 100iterations 8.6070132E-04 3.0738831E-02 at 110iterations 3.7687662E-04 1.3410568E-02 at 120iterations finished qdiffx linear iterations at : 16:20:51 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 3.7687662E-04 1.3410568E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 16:20:52 10.548u 0.423s 0:11.26 97.3% 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 16:20:52 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 = 2355 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: 2.634522 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 2.634522 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2266 net assigned charge : 4.000001 assigned positive charge : 348.1421 centred at (gu) : 91.19769 84.82325 84.52628 assigned negative charge : -344.1427 centred at (gu) : 91.40189 85.37218 84.65651 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 133453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20369 grid for indexing accessible points = 1.400000 m= 62069 mr = 95841 m= 19766 mr = 49531 m= 3951 mr = 15531 m= 313 mr = 2864 m= 11 mr = 167 m= 0 mr = 3 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 55626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 18123 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) : 1.756348 object centre at (A) : 22.03000 6.888500 11.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1838820 0.4504904 midg,1,midg; midg,igrid,midg 0.1412133 -3.1170174E-02 1,midg,midg; igrid,midg,midg 7.2229698E-02 -0.2756478 gauss-seidel spectral radius is 0.9991791 estimated iterations to convergence 276 setup time was (sec) 1.510000 now iterating at: 16:20:54 rms-change max change #iterations 8.329296 301.4973 at 10iterations 4.750556 120.7771 at 20iterations 2.688960 72.77988 at 30iterations 1.519463 33.11823 at 40iterations 0.8561674 20.30552 at 50iterations 0.4817163 10.18952 at 60iterations 0.2708305 6.655746 at 70iterations 0.1518404 3.177902 at 80iterations 8.4775455E-02 1.918777 at 90iterations 4.7426816E-02 1.023260 at 100iterations 2.6612397E-02 0.5363731 at 110iterations 1.4846042E-02 0.3067613 at 120iterations 8.3071394E-03 0.1749725 at 130iterations 4.6306839E-03 9.4930649E-02 at 140iterations 2.5954260E-03 5.5526733E-02 at 150iterations 1.4579712E-03 3.0467987E-02 at 160iterations 8.1657572E-04 1.7185211E-02 at 170iterations 4.6218053E-04 1.1685848E-02 at 180iterations finished qdiffx linear iterations at : 16:21:11 total time elapsed so far: 18.47000 # loops : 180 mean,max change (kT/e) : 4.6218053E-04 1.1685848E-02 energy calculations done at 18.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.65000 DelPhi exited at 16:21:11 18.658u 0.446s 0:19.40 98.4% 0+0k 0+0io 0pf+0w