Sat Oct 8 18:05:49 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 Sat Oct 8 2011 at 18:05:49 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4593 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: 0.5476165 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): -14.89400 45.34200 ymin,ymax (A): -33.98600 30.86300 zmin,zma (A): 17.26300 82.27200 x,y,z range (A): 60.23600 64.84900 65.00900 scale (grids/A): 0.5476165 object centre (A): 15.22400 -1.561501 49.76750 number of atom coordinates read : 4593 total number of charged atoms : 4439 net assigned charge : -10.99997 assigned positive charge : 696.1920 centred at (gu) : 88.90551 89.22723 89.04961 assigned negative charge : -707.1970 centred at (gu) : 88.93711 89.24303 89.02277 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9347 nv = 96 ne = 84 npr = 89256 no. pairs analyzed = 89256 no. exposed pairs = 6084 no. arc points = 43683 no. surface atoms = 2023 nbur = 2570 mkacc time = 0.1500000 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 = 1.568000 m= 442 mr = 4832 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4381 ## 515 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 12114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3026188E-09 -3.4644423E-10 midg,1,midg; midg,igrid,midg -6.6551564E-10 -7.5421819E-10 1,midg,midg; igrid,midg,midg -4.8640370E-10 -8.3394092E-10 gauss-seidel spectral radius is 0.9829465 estimated iterations to convergence 63 setup time was (sec) 0.4900000 now iterating at: 18:05:50 rms-change max change #iterations 9.4873443E-02 13.26204 at 10iterations 6.4923572E-03 1.058872 at 20iterations 5.8561267E-04 7.7420950E-02 at 30iterations 1.2171233E-04 2.1738052E-02 at 40iterations 3.5490917E-05 6.4487457E-03 at 50iterations finished qdiffx linear iterations at : 18:05:53 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 3.5490917E-05 6.4487457E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 18:05:53 3.471u 0.172s 0:03.91 93.0% 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 Sat Oct 8 2011 at 18:05:53 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4593 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: 1.642850 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): -14.89400 45.34200 ymin,ymax (A): -33.98600 30.86300 zmin,zma (A): 17.26300 82.27200 x,y,z range (A): 60.23600 64.84900 65.00900 scale (grids/A): 1.642850 object centre (A): 15.22400 -1.561501 49.76750 number of atom coordinates read : 4593 total number of charged atoms : 4439 net assigned charge : -10.99997 assigned positive charge : 696.1920 centred at (gu) : 86.71491 87.67977 87.14729 assigned negative charge : -707.1970 centred at (gu) : 86.81110 87.72889 87.06850 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 103548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33750 mr = 70306 m= 3710 mr = 23147 m= 128 mr = 1719 m= 0 mr = 9 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.4800000 number of dielectric boundary points 45955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 34035 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) : 0.5476165 object centre at (A) : 15.22400 -1.561501 49.76750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0408851E-02 -2.2969241E-03 midg,1,midg; midg,igrid,midg 9.9980626E-03 2.3895563E-03 1,midg,midg; igrid,midg,midg -8.9748902E-03 -3.8882371E-02 gauss-seidel spectral radius is 0.9983873 estimated iterations to convergence 198 setup time was (sec) 0.7000000 now iterating at: 18:05:54 rms-change max change #iterations 4.414869 173.0884 at 10iterations 1.926697 59.08437 at 20iterations 0.8441678 26.89832 at 30iterations 0.3684230 11.34926 at 40iterations 0.1621099 5.526563 at 50iterations 7.0868120E-02 2.224588 at 60iterations 3.1044183E-02 0.8910828 at 70iterations 1.3699768E-02 0.3854218 at 80iterations 5.9871408E-03 0.1746936 at 90iterations 2.6475254E-03 7.5847626E-02 at 100iterations 1.1681784E-03 3.5358906E-02 at 110iterations 5.2197621E-04 1.5663147E-02 at 120iterations finished qdiffx linear iterations at : 18:06:01 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 5.2197621E-04 1.5663147E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 18:06:02 8.004u 0.196s 0:08.50 96.3% 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 Sat Oct 8 2011 at 18:06:02 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4593 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: 2.464274 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): -14.89400 45.34200 ymin,ymax (A): -33.98600 30.86300 zmin,zma (A): 17.26300 82.27200 x,y,z range (A): 60.23600 64.84900 65.00900 scale (grids/A): 2.464274 object centre (A): 15.22400 -1.561501 49.76750 number of atom coordinates read : 4593 total number of charged atoms : 4439 net assigned charge : -10.99997 assigned positive charge : 696.1920 centred at (gu) : 85.07220 86.51930 85.72057 assigned negative charge : -707.1970 centred at (gu) : 85.21657 86.59343 85.60265 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 239701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 115505 mr = 171577 m= 34369 mr = 91347 m= 5989 mr = 25410 m= 525 mr = 3849 m= 10 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 1.250000 number of dielectric boundary points 103680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 35482 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) : 1.642850 object centre at (A) : 15.22400 -1.561501 49.76750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2401647E-02 -3.5880510E-02 midg,1,midg; midg,igrid,midg 0.1038966 7.7479176E-02 1,midg,midg; igrid,midg,midg 4.4721976E-02 -0.6039065 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.500000 now iterating at: 18:06:04 rms-change max change #iterations 11.55963 321.0027 at 10iterations 6.868393 170.4780 at 20iterations 4.058836 85.83823 at 30iterations 2.378885 47.30360 at 40iterations 1.386928 28.46906 at 50iterations 0.8049735 13.85551 at 60iterations 0.4660664 8.761522 at 70iterations 0.2694293 5.083799 at 80iterations 0.1554687 2.671146 at 90iterations 8.9476526E-02 1.460833 at 100iterations 5.1577855E-02 0.9229145 at 110iterations 2.9696966E-02 0.5333672 at 120iterations 1.7037675E-02 0.2837601 at 130iterations 9.7940499E-03 0.1664772 at 140iterations 5.6315190E-03 9.5155716E-02 at 150iterations 3.2356894E-03 5.4265022E-02 at 160iterations 1.8650834E-03 2.9447556E-02 at 170iterations 1.0763084E-03 1.9343615E-02 at 180iterations finished qdiffx linear iterations at : 18:06:16 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 1.0763084E-03 1.9343615E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 18:06:16 13.530u 0.199s 0:14.05 97.6% 0+0k 0+0io 0pf+0w