Mon Oct 10 10:21:39 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 Mon Oct 10 2011 at 10:21:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 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: 0.5622503 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 0.5622503 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.00003 assigned positive charge : 394.8041 centred at (gu) : 91.89165 91.17344 86.36604 assigned negative charge : -384.8046 centred at (gu) : 91.98208 91.19411 86.20222 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5659 nv = 96 ne = 84 npr = 52061 no. pairs analyzed = 52061 no. exposed pairs = 3974 no. arc points = 28816 no. surface atoms = 1324 nbur = 1368 mkacc time = 0.1200000 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 = 1.540000 m= 291 mr = 2494 m= 0 mr = 10 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2798 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2935826E-09 1.2116522E-09 midg,1,midg; midg,igrid,midg 1.0869280E-09 1.3312249E-09 1,midg,midg; igrid,midg,midg 1.3609748E-09 4.3326465E-10 gauss-seidel spectral radius is 0.9836737 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 10:21:40 rms-change max change #iterations 7.9329528E-02 15.20201 at 10iterations 5.6555378E-03 0.9435158 at 20iterations 4.1072469E-04 7.0647240E-02 at 30iterations 3.4942259E-05 5.3844452E-03 at 40iterations 4.3222258E-06 5.2165985E-04 at 50iterations finished qdiffx linear iterations at : 10:21:42 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.3222258E-06 5.2165985E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 10:21:43 3.430u 0.155s 0:03.92 91.3% 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 10:21:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.686751 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 1.686751 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.00003 assigned positive charge : 394.8041 centred at (gu) : 95.67461 93.51994 79.09766 assigned negative charge : -384.8046 centred at (gu) : 95.94617 93.58228 78.60651 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28816 grid for indexing accessible points = 1.400000 m= 18524 mr = 37527 m= 2099 mr = 11589 m= 72 mr = 874 m= 3 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.5200000 number of dielectric boundary points 31964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19675 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) : 0.5622503 object centre at (A) : 9.150500 16.06750 25.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6897246E-03 9.0680458E-03 midg,1,midg; midg,igrid,midg 1.6582144E-02 1.8350028E-02 1,midg,midg; igrid,midg,midg -1.3347422E-02 1.1193752E-02 gauss-seidel spectral radius is 0.9982774 estimated iterations to convergence 191 setup time was (sec) 0.8300000 now iterating at: 10:21:44 rms-change max change #iterations 3.286307 166.1489 at 10iterations 1.394492 57.04963 at 20iterations 0.5912759 22.14637 at 30iterations 0.2499578 9.087784 at 40iterations 0.1063400 4.116268 at 50iterations 4.5076676E-02 1.636154 at 60iterations 1.9126324E-02 0.6723486 at 70iterations 8.1522949E-03 0.2867985 at 80iterations 3.4768339E-03 0.1324081 at 90iterations 1.4774845E-03 5.2944660E-02 at 100iterations 6.3234108E-04 2.6402950E-02 at 110iterations 2.6940403E-04 1.1664391E-02 at 120iterations finished qdiffx linear iterations at : 10:21:51 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.6940403E-04 1.1664391E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 10:21:51 7.770u 0.268s 0:08.57 93.6% 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 10:21:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 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: 2.530126 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 2.530126 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.00003 assigned positive charge : 394.8041 centred at (gu) : 98.51187 95.27987 73.64647 assigned negative charge : -384.8046 centred at (gu) : 98.91924 95.37327 72.90965 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 141897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28816 grid for indexing accessible points = 1.400000 m= 61917 mr = 92972 m= 18637 mr = 45896 m= 3173 mr = 13159 m= 262 mr = 1813 m= 7 mr = 73 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 1.210000 number of dielectric boundary points 71980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 20349 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) : 1.686751 object centre at (A) : 9.150500 16.06750 25.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6354476E-02 0.1159448 midg,1,midg; midg,igrid,midg 0.2922643 0.2384570 1,midg,midg; igrid,midg,midg -0.5517650 0.1656236 gauss-seidel spectral radius is 0.9991629 estimated iterations to convergence 273 setup time was (sec) 1.510000 now iterating at: 10:21:53 rms-change max change #iterations 8.620467 258.5009 at 10iterations 4.994724 125.2376 at 20iterations 2.848411 82.17863 at 30iterations 1.608499 47.07538 at 40iterations 0.9081720 21.73890 at 50iterations 0.5092854 12.62170 at 60iterations 0.2848755 6.841003 at 70iterations 0.1591231 3.587421 at 80iterations 8.8784650E-02 2.657811 at 90iterations 4.9445428E-02 1.148674 at 100iterations 2.7445216E-02 0.6890259 at 110iterations 1.5293046E-02 0.3507748 at 120iterations 8.4808953E-03 0.1974921 at 130iterations 4.7074687E-03 0.1093349 at 140iterations 2.6125393E-03 5.6385994E-02 at 150iterations 1.4487191E-03 3.2537460E-02 at 160iterations 8.0369593E-04 1.7578125E-02 at 170iterations 4.4561806E-04 9.4325542E-03 at 180iterations finished qdiffx linear iterations at : 10:22:04 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 4.4561806E-04 9.4325542E-03 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 10:22:04 12.168u 0.206s 0:12.75 96.9% 0+0k 0+0io 0pf+0w