Sat Oct 15 14:44:25 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 Sat Oct 15 2011 at 14:44:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5429147 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 0.5429147 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.499966 assigned positive charge : 449.4609 centred at (gu) : 90.56280 89.83183 90.59998 assigned negative charge : -452.9621 centred at (gu) : 90.57905 89.99203 90.70988 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5730 nv = 96 ne = 84 npr = 59935 no. pairs analyzed = 59935 no. exposed pairs = 3987 no. arc points = 27713 no. surface atoms = 1332 nbur = 1666 mkacc time = 0.1600000 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= 204 mr = 2845 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7509 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9878983E-10 -1.0012982E-09 midg,1,midg; midg,igrid,midg 7.9196510E-10 -1.1264795E-09 1,midg,midg; igrid,midg,midg -7.9898331E-11 -3.2951566E-10 gauss-seidel spectral radius is 0.9825155 estimated iterations to convergence 62 setup time was (sec) 0.6800000 now iterating at: 14:44:26 rms-change max change #iterations 7.0889689E-02 13.52868 at 10iterations 4.6211863E-03 0.7595134 at 20iterations 3.0624462E-04 5.5845261E-02 at 30iterations 2.0395433E-05 3.4465790E-03 at 40iterations 1.3825108E-06 2.0980835E-04 at 50iterations finished qdiffx linear iterations at : 14:44:31 total time elapsed so far: 5.260000 # loops : 50 mean,max change (kT/e) : 1.3825108E-06 2.0980835E-04 energy calculations done at 5.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.430000 DelPhi exited at 14:44:31 5.434u 0.443s 0:06.17 95.1% 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 Sat Oct 15 2011 at 14:44:31 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 = 2998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.628744 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 1.628744 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.499966 assigned positive charge : 449.4609 centred at (gu) : 91.68761 89.49457 91.79925 assigned negative charge : -452.9621 centred at (gu) : 91.73686 89.97565 92.12899 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27713 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18217 mr = 41744 m= 1791 mr = 12138 m= 39 mr = 845 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 847 time to turn everything in is 0.5200000 number of dielectric boundary points 28584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21873 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) : 0.5429147 object centre at (A) : 1.610001 -2.287999 -16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3994195E-03 -7.0384745E-03 midg,1,midg; midg,igrid,midg 8.7559558E-03 -1.4290017E-02 1,midg,midg; igrid,midg,midg -3.8208072E-03 -2.4942493E-02 gauss-seidel spectral radius is 0.9981763 estimated iterations to convergence 186 setup time was (sec) 0.8700000 now iterating at: 14:44:33 rms-change max change #iterations 3.305634 158.0344 at 10iterations 1.368734 52.32912 at 20iterations 0.5672587 20.69882 at 30iterations 0.2361730 9.079977 at 40iterations 9.8144494E-02 3.686248 at 50iterations 4.0862620E-02 1.656192 at 60iterations 1.6931035E-02 0.5958424 at 70iterations 7.0456816E-03 0.2717714 at 80iterations 2.9321630E-03 0.1027048 at 90iterations 1.2180858E-03 4.5542717E-02 at 100iterations 5.0662970E-04 1.9184113E-02 at 110iterations 2.1114336E-04 7.8315735E-03 at 120iterations finished qdiffx linear iterations at : 14:44:44 total time elapsed so far: 12.05000 # loops : 120 mean,max change (kT/e) : 2.1114336E-04 7.8315735E-03 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 14:44:44 12.234u 0.520s 0:13.18 96.7% 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 Sat Oct 15 2011 at 14:44:44 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 = 2998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.443116 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 2.443116 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.499966 assigned positive charge : 449.4609 centred at (gu) : 92.53114 89.24163 92.69871 assigned negative charge : -452.9621 centred at (gu) : 92.60515 89.96329 93.19357 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 147270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27713 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63900 mr = 102863 m= 17205 mr = 49406 m= 2726 mr = 12714 m= 203 mr = 1738 m= 5 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2946 time to turn everything in is 1.310000 number of dielectric boundary points 64501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22814 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) : 1.628744 object centre at (A) : 1.610001 -2.287999 -16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1984960E-03 -8.9564495E-02 midg,1,midg; midg,igrid,midg 0.1480222 -0.1926606 1,midg,midg; igrid,midg,midg 0.2085248 -0.7141209 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.700000 now iterating at: 14:44:47 rms-change max change #iterations 8.655573 371.9138 at 10iterations 4.862444 127.6810 at 20iterations 2.714242 66.65118 at 30iterations 1.505906 40.96689 at 40iterations 0.8362229 18.72522 at 50iterations 0.4615723 9.854507 at 60iterations 0.2545016 5.568693 at 70iterations 0.1403452 2.940226 at 80iterations 7.7204660E-02 1.618170 at 90iterations 4.2516038E-02 0.8250465 at 100iterations 2.3319071E-02 0.5186167 at 110iterations 1.2837484E-02 0.2632828 at 120iterations 7.0483070E-03 0.1607742 at 130iterations 3.8691459E-03 8.2477093E-02 at 140iterations 2.1308758E-03 4.3125629E-02 at 150iterations 1.1707946E-03 2.6272058E-02 at 160iterations 6.4171141E-04 1.3717651E-02 at 170iterations 3.5218563E-04 7.6122284E-03 at 180iterations finished qdiffx linear iterations at : 14:45:06 total time elapsed so far: 21.11000 # loops : 180 mean,max change (kT/e) : 3.5218563E-04 7.6122284E-03 energy calculations done at 21.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.28000 DelPhi exited at 14:45:07 21.288u 0.541s 0:22.10 98.7% 0+0k 0+0io 0pf+0w