Sun Oct 9 22:42:29 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 Sun Oct 9 2011 at 22:42:29 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5948105 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 0.5948105 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2603 net assigned charge : 7.025012 assigned positive charge : 419.0836 centred at (gu) : 89.91735 90.29279 90.62814 assigned negative charge : -412.0595 centred at (gu) : 89.99070 90.27602 90.69728 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6314 nv = 96 ne = 84 npr = 54643 no. pairs analyzed = 54643 no. exposed pairs = 3426 no. arc points = 24411 no. surface atoms = 1153 nbur = 1598 mkacc time = 0.1200000 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= 286 mr = 3231 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3200000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2512 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1745700E-09 2.7371683E-10 midg,1,midg; midg,igrid,midg 1.8743984E-09 3.3135723E-09 1,midg,midg; igrid,midg,midg 5.0415743E-09 1.1451074E-10 gauss-seidel spectral radius is 0.9853879 estimated iterations to convergence 68 setup time was (sec) 0.5300000 now iterating at: 22:42:30 rms-change max change #iterations 0.1039485 18.76316 at 10iterations 8.8250143E-03 1.315918 at 20iterations 7.2393322E-04 0.1100488 at 30iterations 6.0663369E-05 9.0112686E-03 at 40iterations 5.1594620E-06 9.2017651E-04 at 50iterations finished qdiffx linear iterations at : 22:42:32 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 5.1594620E-06 9.2017651E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 22:42:33 3.180u 0.141s 0:03.66 90.7% 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 22:42:33 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.784431 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 1.784431 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2603 net assigned charge : 7.025012 assigned positive charge : 419.0836 centred at (gu) : 89.75137 90.87784 91.88362 assigned negative charge : -412.0595 centred at (gu) : 89.97187 90.82787 92.09148 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24411 grid for indexing accessible points = 1.400000 m= 21629 mr = 46141 m= 2842 mr = 15039 m= 148 mr = 1698 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1006 time to turn everything in is 0.5400000 number of dielectric boundary points 30608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20262 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) : 0.5948105 object centre at (A) : -32.57550 -6.082500 41.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8718465E-03 5.9919879E-03 midg,1,midg; midg,igrid,midg 5.9701852E-03 1.5654651E-03 1,midg,midg; igrid,midg,midg 8.6053656E-03 1.6462902E-02 gauss-seidel spectral radius is 0.9984617 estimated iterations to convergence 202 setup time was (sec) 0.8200000 now iterating at: 22:42:34 rms-change max change #iterations 3.836062 184.3556 at 10iterations 1.706571 61.48008 at 20iterations 0.7561211 25.48614 at 30iterations 0.3389047 10.64647 at 40iterations 0.1512313 5.375664 at 50iterations 6.7425102E-02 2.465675 at 60iterations 3.0081054E-02 1.033000 at 70iterations 1.3481174E-02 0.4554653 at 80iterations 6.0058315E-03 0.1921234 at 90iterations 2.6902566E-03 9.6582413E-02 at 100iterations 1.2006129E-03 4.3842316E-02 at 110iterations 5.3660508E-04 1.8466949E-02 at 120iterations finished qdiffx linear iterations at : 22:42:40 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 5.3660508E-04 1.8466949E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 22:42:40 7.082u 0.170s 0:07.58 95.6% 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 22:42:40 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.676647 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 2.676647 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2603 net assigned charge : 7.025012 assigned positive charge : 419.0836 centred at (gu) : 89.62694 91.31646 92.82516 assigned negative charge : -412.0595 centred at (gu) : 89.95779 91.24182 93.13717 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 159673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24411 grid for indexing accessible points = 1.400000 m= 73067 mr = 112482 m= 22752 mr = 57993 m= 4927 mr = 17467 m= 601 mr = 3615 m= 30 mr = 384 m= 0 mr = 17 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3661 time to turn everything in is 1.170000 number of dielectric boundary points 69092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 20816 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) : 1.784431 object centre at (A) : -32.57550 -6.082500 41.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2354949 -0.2421526 midg,1,midg; midg,igrid,midg 0.1001682 -3.3360511E-02 1,midg,midg; igrid,midg,midg -9.9636987E-02 0.2470694 gauss-seidel spectral radius is 0.9992125 estimated iterations to convergence 281 setup time was (sec) 1.480000 now iterating at: 22:42:42 rms-change max change #iterations 9.310390 310.7963 at 10iterations 5.343689 121.6682 at 20iterations 3.034952 74.28432 at 30iterations 1.722468 38.24714 at 40iterations 0.9752634 19.94404 at 50iterations 0.5513795 13.72433 at 60iterations 0.3113860 6.246774 at 70iterations 0.1760049 3.810722 at 80iterations 9.9181108E-02 2.133235 at 90iterations 5.5859189E-02 1.095612 at 100iterations 3.1589270E-02 0.6124020 at 110iterations 1.7783584E-02 0.3766460 at 120iterations 1.0036981E-02 0.1902142 at 130iterations 5.6501022E-03 0.1206970 at 140iterations 3.1888168E-03 6.4178467E-02 at 150iterations 1.7925195E-03 3.3035278E-02 at 160iterations 1.0125360E-03 2.0025253E-02 at 170iterations 5.7154847E-04 1.0855675E-02 at 180iterations finished qdiffx linear iterations at : 22:42:52 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 5.7154847E-04 1.0855675E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 22:42:53 11.926u 0.195s 0:12.39 97.7% 0+0k 0+0io 0pf+0w