Mon Oct 10 00:26:14 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 Mon Oct 10 2011 at 00:26:14 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 !!! WARNING: HIR 120 has a net charge of 0.5140 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 158 has a net charge of 0.5140 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: 0.5042493 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 0.5042493 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.95799 assigned positive charge : 795.5389 centred at (gu) : 89.80018 89.22877 90.26994 assigned negative charge : -808.5038 centred at (gu) : 89.77311 89.39933 90.21500 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8389 nv = 96 ne = 84 npr = 109450 no. pairs analyzed = 109450 no. exposed pairs = 6802 no. arc points = 45623 no. surface atoms = 2298 nbur = 3027 mkacc time = 0.2900000 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= 345 mr = 4324 m= 0 mr = 7 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4375 ## 603 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 11415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4655886E-10 -2.0509785E-11 midg,1,midg; midg,igrid,midg 2.8615033E-10 -4.3216952E-10 1,midg,midg; igrid,midg,midg -2.1276826E-10 -7.7076526E-11 gauss-seidel spectral radius is 0.9799249 estimated iterations to convergence 58 setup time was (sec) 0.8400000 now iterating at: 00:26:15 rms-change max change #iterations 6.6362925E-02 12.64903 at 10iterations 4.2355293E-03 0.6679459 at 20iterations 6.2252441E-04 9.6376419E-02 at 30iterations 1.8347535E-04 2.3561478E-02 at 40iterations 6.4192995E-05 9.0522766E-03 at 50iterations finished qdiffx linear iterations at : 00:26:19 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 6.4192995E-05 9.0522766E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 00:26:20 5.205u 0.458s 0:06.06 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 Mon Oct 10 2011 at 00:26:20 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 !!! WARNING: HIR 120 has a net charge of 0.5140 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 158 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.512748 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 1.512748 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.95799 assigned positive charge : 795.5389 centred at (gu) : 89.39893 87.68430 90.80819 assigned negative charge : -808.5038 centred at (gu) : 89.31895 88.19796 90.64442 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 95598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27894 mr = 65841 m= 2536 mr = 18178 m= 62 mr = 1094 m= 0 mr = 1 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 377 time to turn everything in is 0.8200000 number of dielectric boundary points 40976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 552 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 38610 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) : 0.5042493 object centre at (A) : 3.025001 12.85800 26.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2062293E-03 -2.2932226E-03 midg,1,midg; midg,igrid,midg 2.0976456E-02 -2.4925163E-02 1,midg,midg; igrid,midg,midg -1.4053620E-02 2.0599317E-04 gauss-seidel spectral radius is 0.9980987 estimated iterations to convergence 182 setup time was (sec) 1.140000 now iterating at: 00:26:22 rms-change max change #iterations 3.935722 148.3743 at 10iterations 1.601919 62.60140 at 20iterations 0.6573678 22.52302 at 30iterations 0.2681547 8.853539 at 40iterations 0.1098862 3.583176 at 50iterations 4.5195598E-02 1.563275 at 60iterations 1.8598568E-02 0.5535908 at 70iterations 7.6620807E-03 0.2368851 at 80iterations 3.1904692E-03 9.7992420E-02 at 90iterations 1.3586734E-03 4.3998718E-02 at 100iterations 6.0467899E-04 1.7123222E-02 at 110iterations 2.9864072E-04 9.6588135E-03 at 120iterations finished qdiffx linear iterations at : 00:26:32 total time elapsed so far: 11.42000 # loops : 120 mean,max change (kT/e) : 2.9864072E-04 9.6588135E-03 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 00:26:33 11.598u 0.489s 0:12.49 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 Mon Oct 10 2011 at 00:26:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 !!! WARNING: HIR 120 has a net charge of 0.5140 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 158 has a net charge of 0.5140 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: 2.269122 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 2.269122 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.95799 assigned positive charge : 795.5389 centred at (gu) : 89.09784 86.52593 91.21178 assigned negative charge : -808.5038 centred at (gu) : 88.97836 87.29688 90.96661 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 223009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 99264 mr = 162304 m= 25755 mr = 76664 m= 3717 mr = 18185 m= 193 mr = 2268 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 1357 time to turn everything in is 2.030000 number of dielectric boundary points 92470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 41278 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) : 1.512748 object centre at (A) : 3.025001 12.85800 26.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1545984 -8.2193635E-02 midg,1,midg; midg,igrid,midg 0.5785942 -0.4119872 1,midg,midg; igrid,midg,midg -0.2926689 4.0404506E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 2.530000 now iterating at: 00:26:36 rms-change max change #iterations 10.86757 323.1559 at 10iterations 6.292101 135.9483 at 20iterations 3.606970 83.26839 at 30iterations 2.060441 41.87976 at 40iterations 1.168956 23.79083 at 50iterations 0.6608766 13.46509 at 60iterations 0.3723699 7.713817 at 70iterations 0.2096708 4.311490 at 80iterations 0.1175434 2.215122 at 90iterations 6.5871492E-02 1.276512 at 100iterations 3.6967777E-02 0.6532936 at 110iterations 2.0672079E-02 0.3626213 at 120iterations 1.1547735E-02 0.2182689 at 130iterations 6.4610466E-03 0.1178207 at 140iterations 3.6141188E-03 6.7407131E-02 at 150iterations 2.0212571E-03 3.7399292E-02 at 160iterations 1.1338873E-03 2.2457361E-02 at 170iterations 6.3599704E-04 1.0856628E-02 at 180iterations finished qdiffx linear iterations at : 00:26:55 total time elapsed so far: 21.70000 # loops : 180 mean,max change (kT/e) : 6.3599704E-04 1.0856628E-02 energy calculations done at 21.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.87000 DelPhi exited at 00:26:55 21.872u 0.538s 0:22.72 98.5% 0+0k 0+0io 0pf+0w