Sat Oct 8 18:05:21 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 8 2011 at 18:05:21 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 = 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 : 692.5922 centred at (gu) : 88.90654 89.22581 89.04624 assigned negative charge : -703.5969 centred at (gu) : 88.93889 89.23955 89.01665 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 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 = 0.1600000 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 = 1.568000 m= 442 mr = 4832 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 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 0.4000000 number of grid points assigned charge 12114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3403759E-09 -3.2305514E-10 midg,1,midg; midg,igrid,midg -6.9404804E-10 -7.3382672E-10 1,midg,midg; igrid,midg,midg -4.7710430E-10 -8.3879320E-10 gauss-seidel spectral radius is 0.9829465 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 18:05:22 rms-change max change #iterations 9.3845591E-02 13.43174 at 10iterations 6.4421515E-03 1.056875 at 20iterations 6.1167619E-04 8.3799601E-02 at 30iterations 1.3578433E-04 2.3938179E-02 at 40iterations 4.0204486E-05 7.0924759E-03 at 50iterations finished qdiffx linear iterations at : 18:05:25 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 4.0204486E-05 7.0924759E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 18:05:25 3.588u 0.192s 0:04.10 91.9% 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 18:05:25 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 = 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: 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 : 692.5922 centred at (gu) : 86.71805 87.67548 87.13722 assigned negative charge : -703.5969 centred at (gu) : 86.81637 87.71837 87.05008 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 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 0.4900000 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 0.5900000 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 -1.1095879E-02 -2.1621068E-03 midg,1,midg; midg,igrid,midg 9.7526200E-03 2.5330733E-03 1,midg,midg; igrid,midg,midg -8.8645434E-03 -3.8907319E-02 gauss-seidel spectral radius is 0.9983873 estimated iterations to convergence 198 setup time was (sec) 0.7400000 now iterating at: 18:05:26 rms-change max change #iterations 4.379985 173.0884 at 10iterations 1.911471 59.08440 at 20iterations 0.8372661 26.47095 at 30iterations 0.3655261 11.13398 at 40iterations 0.1608022 5.455499 at 50iterations 7.0315041E-02 2.202729 at 60iterations 3.0796334E-02 0.8920135 at 70iterations 1.3591887E-02 0.3872452 at 80iterations 5.9424974E-03 0.1792533 at 90iterations 2.6309551E-03 7.4539185E-02 at 100iterations 1.1631810E-03 3.4929752E-02 at 110iterations 5.2154937E-04 1.5762329E-02 at 120iterations finished qdiffx linear iterations at : 18:05:35 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 5.2154937E-04 1.5762329E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 18:05:35 9.030u 0.227s 0:09.59 96.4% 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 18:05:35 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 = 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 : 692.5922 centred at (gu) : 85.07690 86.51286 85.70546 assigned negative charge : -703.5969 centred at (gu) : 85.22448 86.57767 85.57501 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 = 0.7200000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 1.240000 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 -2.2644404E-02 -3.4188882E-02 midg,1,midg; midg,igrid,midg 0.1010431 7.9254732E-02 1,midg,midg; igrid,midg,midg 5.0655778E-02 -0.6040603 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.500000 now iterating at: 18:05:37 rms-change max change #iterations 11.48444 321.0013 at 10iterations 6.827388 170.4800 at 20iterations 4.035612 84.59247 at 30iterations 2.365515 47.43824 at 40iterations 1.379591 28.50103 at 50iterations 0.8008401 13.74085 at 60iterations 0.4638294 8.679415 at 70iterations 0.2681612 5.132035 at 80iterations 0.1547846 2.663827 at 90iterations 8.9084670E-02 1.451303 at 100iterations 5.1353183E-02 0.9261332 at 110iterations 2.9566685E-02 0.5238419 at 120iterations 1.6966190E-02 0.2838173 at 130iterations 9.7536501E-03 0.1678848 at 140iterations 5.6089405E-03 9.3032837E-02 at 150iterations 3.2233142E-03 5.4107666E-02 at 160iterations 1.8594125E-03 2.9310226E-02 at 170iterations 1.0736246E-03 1.9152403E-02 at 180iterations finished qdiffx linear iterations at : 18:05:49 total time elapsed so far: 13.57000 # loops : 180 mean,max change (kT/e) : 1.0736246E-03 1.9152403E-02 energy calculations done at 13.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 18:05:49 13.703u 0.221s 0:14.21 97.9% 0+0k 0+0io 0pf+0w