Tue Oct 11 03:42:17 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 Tue Oct 11 2011 at 03:42:17 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5086732 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 0.5086732 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3433 net assigned charge : 11.53903 assigned positive charge : 556.2932 centred at (gu) : 90.49627 89.66831 92.12059 assigned negative charge : -544.7558 centred at (gu) : 90.66852 89.88042 92.28938 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5830 nv = 96 ne = 84 npr = 70527 no. pairs analyzed = 70527 no. exposed pairs = 4766 no. arc points = 33838 no. surface atoms = 1574 nbur = 2017 mkacc time = 0.1900000 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 = 1.680000 m= 208 mr = 2812 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3318 ## 556 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6225999E-10 -2.8181324E-10 midg,1,midg; midg,igrid,midg 5.7965710E-10 -2.1605219E-10 1,midg,midg; igrid,midg,midg 4.0559631E-10 -1.8490794E-10 gauss-seidel spectral radius is 0.9801514 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 03:42:19 rms-change max change #iterations 5.9758469E-02 10.25852 at 10iterations 3.5114640E-03 0.6958799 at 20iterations 3.6822815E-04 7.3970795E-02 at 30iterations 8.1894526E-05 1.6006470E-02 at 40iterations 2.1049484E-05 4.1627884E-03 at 50iterations finished qdiffx linear iterations at : 03:42:23 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 2.1049484E-05 4.1627884E-03 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 03:42:23 4.872u 0.431s 0:05.87 90.2% 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 03:42:23 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.526020 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 1.526020 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3433 net assigned charge : 11.53903 assigned positive charge : 556.2932 centred at (gu) : 91.48785 89.00404 96.36115 assigned negative charge : -544.7558 centred at (gu) : 92.00500 89.64080 96.86816 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19154 mr = 42026 m= 1699 mr = 12635 m= 33 mr = 647 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1286 time to turn everything in is 0.5700000 number of dielectric boundary points 30142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25728 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) : 0.5086732 object centre at (A) : -4.184999 19.46050 77.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4847416E-03 -1.7559141E-02 midg,1,midg; midg,igrid,midg 1.9270100E-02 -6.8861330E-03 1,midg,midg; igrid,midg,midg 1.7459683E-02 2.8791071E-03 gauss-seidel spectral radius is 0.9979712 estimated iterations to convergence 177 setup time was (sec) 0.8700000 now iterating at: 03:42:25 rms-change max change #iterations 3.194369 154.2054 at 10iterations 1.264067 49.02514 at 20iterations 0.5009620 20.97449 at 30iterations 0.1987426 7.056293 at 40iterations 7.8619815E-02 2.729242 at 50iterations 3.1290583E-02 1.135759 at 60iterations 1.2474461E-02 0.4468975 at 70iterations 4.9728975E-03 0.2069283 at 80iterations 1.9967046E-03 7.2479248E-02 at 90iterations 8.1272441E-04 3.0128479E-02 at 100iterations 3.4026237E-04 1.3458252E-02 at 110iterations 1.5157106E-04 6.2313080E-03 at 120iterations finished qdiffx linear iterations at : 03:42:34 total time elapsed so far: 10.71000 # loops : 120 mean,max change (kT/e) : 1.5157106E-04 6.2313080E-03 energy calculations done at 10.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 03:42:35 10.877u 0.479s 0:12.01 94.4% 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 03:42:35 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.289030 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 2.289030 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3433 net assigned charge : 11.53903 assigned positive charge : 556.2932 centred at (gu) : 92.23151 88.50568 99.54137 assigned negative charge : -544.7558 centred at (gu) : 93.00747 89.46109 100.3022 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 149826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 66995 mr = 103127 m= 17668 mr = 51595 m= 2384 mr = 12816 m= 91 mr = 1298 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 4325 time to turn everything in is 1.330000 number of dielectric boundary points 68123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 27395 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) : 1.526020 object centre at (A) : -4.184999 19.46050 77.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1535706 -0.4574850 midg,1,midg; midg,igrid,midg 0.3206034 -0.1231260 1,midg,midg; igrid,midg,midg 0.2944475 5.1637292E-02 gauss-seidel spectral radius is 0.9990855 estimated iterations to convergence 261 setup time was (sec) 1.670000 now iterating at: 03:42:37 rms-change max change #iterations 8.774136 294.1476 at 10iterations 4.936537 128.2709 at 20iterations 2.737891 108.4428 at 30iterations 1.510051 39.79263 at 40iterations 0.8297110 20.67511 at 50iterations 0.4548866 12.00468 at 60iterations 0.2479176 5.663376 at 70iterations 0.1350980 3.291516 at 80iterations 7.3545903E-02 1.725290 at 90iterations 3.9899979E-02 0.9479122 at 100iterations 2.1607587E-02 0.4538956 at 110iterations 1.1733881E-02 0.2404041 at 120iterations 6.3548167E-03 0.1374817 at 130iterations 3.4404958E-03 7.3272705E-02 at 140iterations 1.8618007E-03 4.1568995E-02 at 150iterations 1.0096944E-03 2.1724701E-02 at 160iterations 5.4629275E-04 1.2527466E-02 at 170iterations 2.9776347E-04 6.1492920E-03 at 180iterations finished qdiffx linear iterations at : 03:42:54 total time elapsed so far: 18.55000 # loops : 180 mean,max change (kT/e) : 2.9776347E-04 6.1492920E-03 energy calculations done at 18.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.72000 DelPhi exited at 03:42:57 18.729u 0.510s 0:21.38 89.9% 0+0k 0+0io 0pf+0w