Sun Oct 9 03:10:40 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 03:10:40 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 !!! WARNING: SEP 530 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5194427 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 0.5194427 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4433 net assigned charge : 17.02499 assigned positive charge : 681.2197 centred at (gu) : 90.28173 87.44852 90.69357 assigned negative charge : -664.2000 centred at (gu) : 90.31570 87.45724 90.74738 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7783 nv = 96 ne = 84 npr = 92851 no. pairs analyzed = 92851 no. exposed pairs = 5968 no. arc points = 40472 no. surface atoms = 2045 nbur = 2554 mkacc time = 0.2600000 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 = 1.624000 m= 314 mr = 3920 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3972 ## 558 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5178722E-10 1.9604443E-10 midg,1,midg; midg,igrid,midg 7.3919798E-10 1.7230213E-10 1,midg,midg; igrid,midg,midg 4.3851939E-10 2.5257038E-10 gauss-seidel spectral radius is 0.9810346 estimated iterations to convergence 60 setup time was (sec) 0.7900000 now iterating at: 03:10:41 rms-change max change #iterations 7.1088552E-02 12.05278 at 10iterations 5.9457049E-03 0.8633461 at 20iterations 1.3781876E-03 0.2023544 at 30iterations 4.2447861E-04 6.1298370E-02 at 40iterations 1.3288332E-04 1.8962860E-02 at 50iterations finished qdiffx linear iterations at : 03:10:45 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.3288332E-04 1.8962860E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 03:10:45 4.320u 0.248s 0:04.89 93.2% 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 Sun Oct 9 2011 at 03:10:45 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 !!! WARNING: SEP 530 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.558328 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 1.558328 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4433 net assigned charge : 17.02499 assigned positive charge : 681.2197 centred at (gu) : 90.84345 82.34396 92.07902 assigned negative charge : -664.2000 centred at (gu) : 90.94684 82.37144 92.24174 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27197 mr = 57327 m= 2669 mr = 18376 m= 77 mr = 1245 m= 0 mr = 1 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 214 time to turn everything in is 0.7600000 number of dielectric boundary points 39014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 503 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 33489 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) : 0.5194427 object centre at (A) : 247.7680 105.9555 -37.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1625923E-02 7.2880280E-03 midg,1,midg; midg,igrid,midg 3.3192545E-02 1.1809839E-02 1,midg,midg; igrid,midg,midg 2.6509690E-03 1.9096034E-03 gauss-seidel spectral radius is 0.9981701 estimated iterations to convergence 186 setup time was (sec) 1.080000 now iterating at: 03:10:47 rms-change max change #iterations 3.771017 139.1889 at 10iterations 1.559926 53.15904 at 20iterations 0.6472964 22.87289 at 30iterations 0.2687545 10.34258 at 40iterations 0.1121832 3.610484 at 50iterations 4.6887528E-02 1.550789 at 60iterations 1.9821128E-02 0.6786537 at 70iterations 8.5074753E-03 0.2867413 at 80iterations 3.8186302E-03 0.1206970 at 90iterations 1.8373829E-03 6.1969757E-02 at 100iterations 9.7257772E-04 3.2569885E-02 at 110iterations 5.6570448E-04 1.7219543E-02 at 120iterations finished qdiffx linear iterations at : 03:10:55 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 5.6570448E-04 1.7219543E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 03:10:56 9.732u 0.259s 0:10.33 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 03:10:56 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 !!! WARNING: SEP 530 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.337492 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 2.337492 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4433 net assigned charge : 17.02499 assigned positive charge : 681.2197 centred at (gu) : 91.26460 78.51540 93.11818 assigned negative charge : -664.2000 centred at (gu) : 91.42012 78.55705 93.36273 start vw surface at 0.2300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 199623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 92321 mr = 140704 m= 26852 mr = 71669 m= 4276 mr = 19991 m= 274 mr = 2646 m= 2 mr = 93 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 717 time to turn everything in is 1.680000 number of dielectric boundary points 88246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 35390 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) : 1.558328 object centre at (A) : 247.7680 105.9555 -37.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5095546 5.3735930E-02 midg,1,midg; midg,igrid,midg 0.4656862 0.1738920 1,midg,midg; igrid,midg,midg 5.3447530E-02 6.8793963E-03 gauss-seidel spectral radius is 0.9991777 estimated iterations to convergence 275 setup time was (sec) 2.030000 now iterating at: 03:10:58 rms-change max change #iterations 10.24250 345.1878 at 10iterations 5.916683 151.1109 at 20iterations 3.391223 77.78783 at 30iterations 1.929407 41.08291 at 40iterations 1.091437 22.89755 at 50iterations 0.6163155 12.57665 at 60iterations 0.3478475 6.453573 at 70iterations 0.1950065 3.941090 at 80iterations 0.1095248 2.097073 at 90iterations 6.1421670E-02 1.141768 at 100iterations 3.4352943E-02 0.6178741 at 110iterations 1.9276122E-02 0.3514271 at 120iterations 1.0800739E-02 0.2088823 at 130iterations 6.0724420E-03 0.1062374 at 140iterations 3.4275232E-03 6.2686920E-02 at 150iterations 1.9491382E-03 4.3413162E-02 at 160iterations 1.1253689E-03 2.2186279E-02 at 170iterations 6.6468026E-04 1.3856888E-02 at 180iterations finished qdiffx linear iterations at : 03:11:12 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 6.6468026E-04 1.3856888E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 03:11:12 15.864u 0.281s 0:16.42 98.2% 0+0k 0+0io 0pf+0w