Tue Oct 11 06:49:50 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 06:49:50 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5339813 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): -20.57500 46.09400 ymin,ymax (A): 22.00000 78.86000 zmin,zma (A): -71.34900 -24.20600 x,y,z range (A): 66.66900 56.86000 47.14300 scale (grids/A): 0.5339813 object centre (A): 12.75950 50.43000 -47.77750 number of atom coordinates read : 2942 total number of charged atoms : 2800 net assigned charge : -3.960994 assigned positive charge : 428.4047 centred at (gu) : 89.33373 89.79986 89.88250 assigned negative charge : -432.3662 centred at (gu) : 89.29244 89.89687 89.87958 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5462 nv = 96 ne = 84 npr = 60848 no. pairs analyzed = 60848 no. exposed pairs = 3684 no. arc points = 25925 no. surface atoms = 1249 nbur = 1693 mkacc time = 0.1300000 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 = 1.596000 m= 193 mr = 2842 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 2809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2574 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6877820E-10 -1.3611766E-10 midg,1,midg; midg,igrid,midg 2.5250996E-10 -5.2602561E-10 1,midg,midg; igrid,midg,midg -3.8057163E-10 1.2338971E-11 gauss-seidel spectral radius is 0.9819266 estimated iterations to convergence 61 setup time was (sec) 0.5800000 now iterating at: 06:49:51 rms-change max change #iterations 6.6456445E-02 11.72968 at 10iterations 4.1298484E-03 0.7832327 at 20iterations 2.8882176E-04 4.7389984E-02 at 30iterations 3.3835473E-05 8.8186264E-03 at 40iterations 6.8739041E-06 1.8720627E-03 at 50iterations finished qdiffx linear iterations at : 06:49:54 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 6.8739041E-06 1.8720627E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 06:49:55 3.157u 0.149s 0:04.63 71.0% 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 06:49:55 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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: 1.601944 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): -20.57500 46.09400 ymin,ymax (A): 22.00000 78.86000 zmin,zma (A): -71.34900 -24.20600 x,y,z range (A): 66.66900 56.86000 47.14300 scale (grids/A): 1.601944 object centre (A): 12.75950 50.43000 -47.77750 number of atom coordinates read : 2942 total number of charged atoms : 2800 net assigned charge : -3.960994 assigned positive charge : 428.4047 centred at (gu) : 88.00060 89.39907 89.64696 assigned negative charge : -432.3662 centred at (gu) : 87.87666 89.69035 89.63843 start vw surface at 0.2000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25925 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18816 mr = 40719 m= 1887 mr = 13129 m= 45 mr = 920 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 331 time to turn everything in is 0.4800000 number of dielectric boundary points 26195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 21329 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) : 0.5339813 object centre at (A) : 12.75950 50.43000 -47.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1047448E-03 5.1805051E-03 midg,1,midg; midg,igrid,midg -1.2193626E-03 1.5911175E-03 1,midg,midg; igrid,midg,midg -1.3654554E-02 -2.5885727E-02 gauss-seidel spectral radius is 0.9981118 estimated iterations to convergence 183 setup time was (sec) 0.7400000 now iterating at: 06:49:56 rms-change max change #iterations 3.151785 146.4724 at 10iterations 1.287136 53.08811 at 20iterations 0.5277567 20.95992 at 30iterations 0.2159246 7.718317 at 40iterations 8.8780127E-02 3.205248 at 50iterations 3.6439288E-02 1.412067 at 60iterations 1.5023400E-02 0.5279331 at 70iterations 6.1864662E-03 0.2303954 at 80iterations 2.5685860E-03 9.8836899E-02 at 90iterations 1.0747327E-03 4.1488647E-02 at 100iterations 4.5824348E-04 2.0312309E-02 at 110iterations 2.0307863E-04 8.5004568E-03 at 120iterations finished qdiffx linear iterations at : 06:50:02 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 2.0307863E-04 8.5004568E-03 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 06:50:03 6.751u 0.170s 0:07.68 90.1% 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 06:50:03 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.402916 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): -20.57500 46.09400 ymin,ymax (A): 22.00000 78.86000 zmin,zma (A): -71.34900 -24.20600 x,y,z range (A): 66.66900 56.86000 47.14300 scale (grids/A): 2.402916 object centre (A): 12.75950 50.43000 -47.77750 number of atom coordinates read : 2942 total number of charged atoms : 2800 net assigned charge : -3.960994 assigned positive charge : 428.4047 centred at (gu) : 87.00076 89.09850 89.47034 assigned negative charge : -432.3662 centred at (gu) : 86.81498 89.53551 89.45748 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 139977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25925 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64595 mr = 99584 m= 18631 mr = 51390 m= 2796 mr = 14240 m= 149 mr = 1855 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 1134 time to turn everything in is 1.060000 number of dielectric boundary points 59012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 22371 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) : 1.601944 object centre at (A) : 12.75950 50.43000 -47.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7846809E-02 0.1005911 midg,1,midg; midg,igrid,midg -1.5396628E-02 4.4362321E-02 1,midg,midg; igrid,midg,midg -0.2187875 -0.7449958 gauss-seidel spectral radius is 0.9991152 estimated iterations to convergence 266 setup time was (sec) 1.340000 now iterating at: 06:50:04 rms-change max change #iterations 8.151353 322.7322 at 10iterations 4.506796 104.8839 at 20iterations 2.488282 57.01752 at 30iterations 1.367678 32.09229 at 40iterations 0.7492330 16.09608 at 50iterations 0.4114160 9.347631 at 60iterations 0.2241334 4.664162 at 70iterations 0.1223814 2.805737 at 80iterations 6.6848747E-02 1.445442 at 90iterations 3.6501233E-02 0.8583708 at 100iterations 1.9845877E-02 0.4020119 at 110iterations 1.0840004E-02 0.2524052 at 120iterations 5.9142518E-03 0.1237488 at 130iterations 3.2149833E-03 6.8481445E-02 at 140iterations 1.7498167E-03 3.5293579E-02 at 150iterations 9.5450948E-04 1.9369125E-02 at 160iterations 5.1912363E-04 1.1179924E-02 at 170iterations 2.8333915E-04 6.3965321E-03 at 180iterations finished qdiffx linear iterations at : 06:50:14 total time elapsed so far: 10.52000 # loops : 180 mean,max change (kT/e) : 2.8333915E-04 6.3965321E-03 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 06:50:14 10.700u 0.158s 0:11.27 96.2% 0+0k 0+0io 0pf+0w