Thu Jan 19 13:32:58 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:58 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 0.4396908 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): 3.760000 84.72600 ymin,ymax (A): -67.53400 12.05400 zmin,zma (A): -42.21800 24.91600 x,y,z range (A): 80.96600 79.58801 67.13400 scale (grids/A): 0.4396908 object centre (A): 44.24300 -27.74000 -8.650999 number of atom coordinates read : 6895 total number of charged atoms : 6724 net assigned charge : 2.200047 assigned positive charge : 1054.518 centred at (gu) : 88.23747 89.97558 89.86407 assigned negative charge : -1052.327 centred at (gu) : 88.14746 89.92030 89.93959 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7884 nv = 96 ne = 84 npr = 137799 no. pairs analyzed = 137799 no. exposed pairs = 9030 no. arc points = 61723 no. surface atoms = 3017 nbur = 3878 mkacc time = 0.2400000 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 = 1.904000 m= 234 mr = 3711 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4400000 number of dielectric boundary points 4405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5350 ## 1129 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 11068 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8097606E-12 -7.3035831E-12 midg,1,midg; midg,igrid,midg -5.3284569E-12 7.1203941E-12 1,midg,midg; igrid,midg,midg -1.6090160E-11 6.4509053E-12 gauss-seidel spectral radius is 0.9737520 estimated iterations to convergence 51 setup time was (sec) 0.6600000 now iterating at: 13:32:59 rms-change max change #iterations 3.3631321E-02 6.010193 at 10iterations 1.8255292E-03 0.2607803 at 20iterations 4.8657204E-04 6.5413475E-02 at 30iterations 1.8027794E-04 2.4381638E-02 at 40iterations 6.7903216E-05 9.2229843E-03 at 50iterations finished qdiffx linear iterations at : 13:33:05 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 6.7903216E-05 9.2229843E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 13:33:05 4.122u 0.215s 0:07.65 56.6% 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 Thu Jan 19 2012 at 13:33:07 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 1.319072 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): 3.760000 84.72600 ymin,ymax (A): -67.53400 12.05400 zmin,zma (A): -42.21800 24.91600 x,y,z range (A): 80.96600 79.58801 67.13400 scale (grids/A): 1.319072 object centre (A): 44.24300 -27.74000 -8.650999 number of atom coordinates read : 6895 total number of charged atoms : 6724 net assigned charge : 2.200047 assigned positive charge : 1054.518 centred at (gu) : 84.71059 89.92474 89.59029 assigned negative charge : -1052.327 centred at (gu) : 84.44186 89.76027 89.81821 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 92776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 21477 mr = 60998 m= 1079 mr = 12533 m= 10 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1613 time to turn everything in is 0.4900000 number of dielectric boundary points 41576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1137 ## 35 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 47169 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) : 0.4396908 object centre at (A) : 44.24300 -27.74000 -8.650999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9264889E-03 -3.7347011E-03 midg,1,midg; midg,igrid,midg 7.9728831E-03 9.2130108E-03 1,midg,midg; igrid,midg,midg -1.7348856E-02 4.6407548E-03 gauss-seidel spectral radius is 0.9975539 estimated iterations to convergence 161 setup time was (sec) 0.7300000 now iterating at: 13:33:09 rms-change max change #iterations 3.280640 147.5508 at 10iterations 1.187136 38.41294 at 20iterations 0.4318489 14.06102 at 30iterations 0.1559141 5.875248 at 40iterations 5.6924473E-02 1.951992 at 50iterations 2.0662883E-02 0.7652240 at 60iterations 7.5993682E-03 0.3322220 at 70iterations 2.8717371E-03 9.8550797E-02 at 80iterations 1.1680695E-03 4.1320801E-02 at 90iterations 5.5450620E-04 1.9897461E-02 at 100iterations 3.2009571E-04 9.6893311E-03 at 110iterations 2.0785991E-04 6.1492920E-03 at 120iterations finished qdiffx linear iterations at : 13:33:24 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.0785991E-04 6.1492920E-03 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 13:33:25 8.283u 0.205s 0:17.84 47.5% 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 Thu Jan 19 2012 at 13:33:25 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 1.978608 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): 3.760000 84.72600 ymin,ymax (A): -67.53400 12.05400 zmin,zma (A): -42.21800 24.91600 x,y,z range (A): 80.96600 79.58801 67.13400 scale (grids/A): 1.978608 object centre (A): 44.24300 -27.74000 -8.650999 number of atom coordinates read : 6895 total number of charged atoms : 6724 net assigned charge : 2.200047 assigned positive charge : 1054.518 centred at (gu) : 82.06572 89.88660 89.38494 assigned negative charge : -1052.327 centred at (gu) : 81.66280 89.64017 89.72723 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 217685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 84154 mr = 152296 m= 14717 mr = 61748 m= 1121 mr = 9119 m= 25 mr = 447 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 5466 time to turn everything in is 1.160000 number of dielectric boundary points 94092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 53127 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) : 1.319072 object centre at (A) : 44.24300 -27.74000 -8.650999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1519896E-02 -9.1037430E-02 midg,1,midg; midg,igrid,midg 0.3362355 0.2765452 1,midg,midg; igrid,midg,midg -0.6159138 0.1344978 gauss-seidel spectral radius is 0.9990364 estimated iterations to convergence 255 setup time was (sec) 1.460000 now iterating at: 13:33:33 rms-change max change #iterations 10.03358 287.5876 at 10iterations 5.557725 138.4802 at 20iterations 3.049603 81.75832 at 30iterations 1.662796 39.00041 at 40iterations 0.9000969 24.06488 at 50iterations 0.4851892 11.06877 at 60iterations 0.2608450 5.784659 at 70iterations 0.1399313 3.021694 at 80iterations 7.5030133E-02 1.556281 at 90iterations 4.0117115E-02 0.8291473 at 100iterations 2.1456689E-02 0.4551468 at 110iterations 1.1458296E-02 0.2525234 at 120iterations 6.1173849E-03 0.1287384 at 130iterations 3.2646761E-03 7.1578264E-02 at 140iterations 1.7433978E-03 3.5117626E-02 at 150iterations 9.3405368E-04 1.9519806E-02 at 160iterations 5.0413242E-04 1.0766983E-02 at 170iterations 2.7541447E-04 6.3171387E-03 at 180iterations finished qdiffx linear iterations at : 13:34:05 total time elapsed so far: 14.76000 # loops : 180 mean,max change (kT/e) : 2.7541447E-04 6.3171387E-03 energy calculations done at 14.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 13:34:06 14.890u 0.261s 0:40.43 37.4% 0+0k 0+0io 0pf+0w