Mon Oct 10 17:02:25 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 Mon Oct 10 2011 at 17:02:25 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 = 2790 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: 0.5909891 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 0.5909891 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.499970 assigned positive charge : 417.7922 centred at (gu) : 89.15272 89.73143 89.26326 assigned negative charge : -420.2934 centred at (gu) : 89.15794 89.54787 89.10234 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6470 nv = 96 ne = 84 npr = 55943 no. pairs analyzed = 55943 no. exposed pairs = 3760 no. arc points = 26448 no. surface atoms = 1269 nbur = 1521 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 = 1.456000 m= 297 mr = 3230 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6595600E-09 3.3324501E-09 midg,1,midg; midg,igrid,midg -6.7135582E-09 4.3271293E-09 1,midg,midg; igrid,midg,midg -6.9231781E-10 -7.3329914E-10 gauss-seidel spectral radius is 0.9852079 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 17:02:26 rms-change max change #iterations 0.1016776 14.50722 at 10iterations 8.2101440E-03 1.265976 at 20iterations 6.7241013E-04 0.1017761 at 30iterations 5.5317556E-05 8.8500977E-03 at 40iterations 4.5081201E-06 6.4086914E-04 at 50iterations finished qdiffx linear iterations at : 17:02:28 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.5081201E-06 6.4086914E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 17:02:30 3.115u 0.149s 0:04.87 66.7% 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 Mon Oct 10 2011 at 17:02:30 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 = 2790 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: 1.772967 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 1.772967 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.499970 assigned positive charge : 417.7922 centred at (gu) : 87.45747 89.19299 87.78892 assigned negative charge : -420.2934 centred at (gu) : 87.47358 88.64334 87.30666 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26448 grid for indexing accessible points = 1.400000 m= 22590 mr = 46448 m= 2759 mr = 15426 m= 91 mr = 1441 m= 0 mr = 16 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 173 time to turn everything in is 0.5000000 number of dielectric boundary points 32409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20655 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) : 0.5909891 object centre at (A) : 18.70900 -4.518000 -17.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5008317E-02 8.1940489E-03 midg,1,midg; midg,igrid,midg -1.1268860E-02 6.5696323E-03 1,midg,midg; igrid,midg,midg 6.1810832E-03 -1.4014122E-03 gauss-seidel spectral radius is 0.9984531 estimated iterations to convergence 202 setup time was (sec) 0.7900000 now iterating at: 17:02:31 rms-change max change #iterations 3.852169 207.0208 at 10iterations 1.707852 68.98883 at 20iterations 0.7624160 25.73137 at 30iterations 0.3398024 11.89906 at 40iterations 0.1520006 5.183093 at 50iterations 6.7701951E-02 2.224908 at 60iterations 3.0242277E-02 0.9655467 at 70iterations 1.3498019E-02 0.4612732 at 80iterations 6.0131247E-03 0.2107911 at 90iterations 2.6843084E-03 8.9366913E-02 at 100iterations 1.1985699E-03 3.9959431E-02 at 110iterations 5.3332938E-04 1.7925262E-02 at 120iterations finished qdiffx linear iterations at : 17:02:38 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 5.3332938E-04 1.7925262E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 17:02:39 7.877u 0.183s 0:09.08 88.6% 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 17:02:40 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 = 2790 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: 2.659451 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 2.659451 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.499970 assigned positive charge : 417.7922 centred at (gu) : 86.18604 88.78962 86.68321 assigned negative charge : -420.2934 centred at (gu) : 86.21038 87.96492 85.95995 start vw surface at 0.2000000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26448 grid for indexing accessible points = 1.400000 m= 75789 mr = 113540 m= 23514 mr = 59404 m= 4541 mr = 17740 m= 398 mr = 3074 m= 5 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 1.210000 number of dielectric boundary points 73218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 21186 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) : 1.772967 object centre at (A) : 18.70900 -4.518000 -17.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2819072 0.1244418 midg,1,midg; midg,igrid,midg -0.1006149 6.1744381E-02 1,midg,midg; igrid,midg,midg 0.1359625 0.3343754 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 1.490000 now iterating at: 17:02:41 rms-change max change #iterations 9.523374 336.7074 at 10iterations 5.573179 148.3332 at 20iterations 3.214877 79.71768 at 30iterations 1.850493 42.86782 at 40iterations 1.059941 22.96151 at 50iterations 0.6059805 12.82949 at 60iterations 0.3455250 7.966783 at 70iterations 0.1968694 4.803571 at 80iterations 0.1122444 2.483810 at 90iterations 6.3782126E-02 1.212410 at 100iterations 3.6216695E-02 0.7014465 at 110iterations 2.0557722E-02 0.4242077 at 120iterations 1.1704374E-02 0.2211647 at 130iterations 6.6396864E-03 0.1432996 at 140iterations 3.7673637E-03 7.2475433E-02 at 150iterations 2.1420196E-03 3.9995670E-02 at 160iterations 1.2144416E-03 2.5058746E-02 at 170iterations 6.8857300E-04 1.3051271E-02 at 180iterations finished qdiffx linear iterations at : 17:02:51 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 6.8857300E-04 1.3051271E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 17:02:52 11.802u 0.172s 0:12.69 94.3% 0+0k 0+0io 0pf+0w