Sun Oct 9 16:52:40 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+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 Sun Oct 9 2011 at 16:52:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 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: 0.5215505 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 0.5215505 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 809.6924 centred at (gu) : 90.14198 89.75282 89.73769 assigned negative charge : -796.6985 centred at (gu) : 90.08163 89.57082 89.82586 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9366 nv = 96 ne = 84 npr = 104613 no. pairs analyzed = 104613 no. exposed pairs = 7092 no. arc points = 50188 no. surface atoms = 2331 nbur = 3019 mkacc time = 0.2800000 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 = 1.652000 m= 323 mr = 4716 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.5400000 number of dielectric boundary points 4968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4936 ## 775 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 12607 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4776213E-10 -1.0076986E-10 midg,1,midg; midg,igrid,midg -5.9240934E-10 1.0446642E-09 1,midg,midg; igrid,midg,midg 2.0762284E-11 5.9520089E-10 gauss-seidel spectral radius is 0.9812482 estimated iterations to convergence 60 setup time was (sec) 0.8700000 now iterating at: 16:52:41 rms-change max change #iterations 8.3943389E-02 11.49249 at 10iterations 8.4571280E-03 1.310623 at 20iterations 2.1773621E-03 0.2694397 at 30iterations 7.0757268E-04 8.2077026E-02 at 40iterations 2.4073025E-04 2.7019501E-02 at 50iterations finished qdiffx linear iterations at : 16:52:46 total time elapsed so far: 5.330000 # loops : 50 mean,max change (kT/e) : 2.4073025E-04 2.7019501E-02 energy calculations done at 5.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 16:52:46 5.488u 0.531s 0:06.29 95.5% 0+0k 0+0io 6pf+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 16:52:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 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: 1.564652 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 1.564652 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 809.6924 centred at (gu) : 90.42454 89.25710 89.21104 assigned negative charge : -796.6985 centred at (gu) : 90.24451 88.71208 89.47699 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 105474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30649 mr = 70981 m= 2807 mr = 20039 m= 59 mr = 1229 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.8700000 number of dielectric boundary points 46740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 705 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 39259 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) : 0.5215505 object centre at (A) : 11.10200 -9.819499 39.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8108371E-02 1.5099341E-02 midg,1,midg; midg,igrid,midg -1.7778886E-02 3.5658941E-02 1,midg,midg; igrid,midg,midg -1.5381799E-02 2.3505537E-02 gauss-seidel spectral radius is 0.9982787 estimated iterations to convergence 191 setup time was (sec) 1.220000 now iterating at: 16:52:48 rms-change max change #iterations 4.285287 168.3928 at 10iterations 1.818730 64.54090 at 20iterations 0.7733897 22.37640 at 30iterations 0.3306229 10.56838 at 40iterations 0.1417452 4.055286 at 50iterations 6.0735606E-02 1.723030 at 60iterations 2.6206456E-02 0.7999028 at 70iterations 1.1529840E-02 0.3383484 at 80iterations 5.2169953E-03 0.1593704 at 90iterations 2.5034335E-03 8.1481934E-02 at 100iterations 1.3001796E-03 3.7687302E-02 at 110iterations 7.4003718E-04 1.9546509E-02 at 120iterations finished qdiffx linear iterations at : 16:53:00 total time elapsed so far: 13.00000 # loops : 120 mean,max change (kT/e) : 7.4003718E-04 1.9546509E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 16:53:00 13.155u 0.588s 0:14.00 98.0% 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 Sun Oct 9 2011 at 16:53:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 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: 2.346977 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 2.346977 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 809.6924 centred at (gu) : 90.63605 88.88511 88.81618 assigned negative charge : -796.6985 centred at (gu) : 90.36656 88.06796 89.21550 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 245439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108965 mr = 174870 m= 27868 mr = 83608 m= 4091 mr = 19959 m= 221 mr = 2526 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 1156 time to turn everything in is 2.210000 number of dielectric boundary points 105562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 41426 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) : 1.564652 object centre at (A) : 11.10200 -9.819499 39.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6506540 0.2697352 midg,1,midg; midg,igrid,midg -0.3239787 0.5660304 1,midg,midg; igrid,midg,midg -0.4472940 0.3628611 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 2.640000 now iterating at: 16:53:04 rms-change max change #iterations 11.45969 307.6530 at 10iterations 6.802555 171.3900 at 20iterations 4.007009 88.83221 at 30iterations 2.341329 49.35218 at 40iterations 1.357857 29.12853 at 50iterations 0.7870736 15.84407 at 60iterations 0.4548419 9.270153 at 70iterations 0.2615691 4.871658 at 80iterations 0.1506222 3.087792 at 90iterations 8.6460747E-02 1.550167 at 100iterations 4.9611192E-02 0.8978450 at 110iterations 2.8436933E-02 0.4980640 at 120iterations 1.6347440E-02 0.2955704 at 130iterations 9.3836728E-03 0.1731911 at 140iterations 5.3948602E-03 9.2098236E-02 at 150iterations 3.1136626E-03 6.3007355E-02 at 160iterations 1.8173035E-03 2.8898239E-02 at 170iterations 1.0769560E-03 1.9493103E-02 at 180iterations finished qdiffx linear iterations at : 16:53:24 total time elapsed so far: 23.08000 # loops : 180 mean,max change (kT/e) : 1.0769560E-03 1.9493103E-02 energy calculations done at 23.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.25000 DelPhi exited at 16:53:25 23.250u 0.591s 0:24.12 98.8% 0+0k 0+0io 0pf+0w