Sat Oct 8 17:27:17 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 17:27:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5513141 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 0.5513141 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271986 assigned positive charge : 525.4031 centred at (gu) : 90.14879 90.04132 89.47058 assigned negative charge : -530.6769 centred at (gu) : 90.17649 90.03384 89.44089 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6906 nv = 96 ne = 84 npr = 69842 no. pairs analyzed = 69842 no. exposed pairs = 4331 no. arc points = 29289 no. surface atoms = 1467 nbur = 2002 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= 276 mr = 3711 m= 2 mr = 25 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 0.3800000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2974 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8501389E-10 -1.0360456E-10 midg,1,midg; midg,igrid,midg -4.6957038E-10 -3.3266395E-10 1,midg,midg; igrid,midg,midg -1.3056432E-10 -6.9529382E-10 gauss-seidel spectral radius is 0.9830694 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 17:27:18 rms-change max change #iterations 8.8580988E-02 16.22662 at 10iterations 6.1197081E-03 0.8464127 at 20iterations 5.2351120E-04 8.5049629E-02 at 30iterations 9.2865841E-05 1.5990257E-02 at 40iterations 2.5264095E-05 4.9037933E-03 at 50iterations finished qdiffx linear iterations at : 17:27:21 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 2.5264095E-05 4.9037933E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 17:27:21 3.277u 0.161s 0:03.76 91.2% 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 17:27:21 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.653942 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 1.653942 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271986 assigned positive charge : 525.4031 centred at (gu) : 90.44562 90.12289 88.41089 assigned negative charge : -530.6769 centred at (gu) : 90.52898 90.10134 88.32247 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25433 mr = 52841 m= 2886 mr = 18018 m= 87 mr = 1506 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 306 time to turn everything in is 0.5800000 number of dielectric boundary points 31942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25535 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) : 0.5513141 object centre at (A) : 65.71300 48.39750 1.662000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3916173E-03 -4.3301871E-03 midg,1,midg; midg,igrid,midg 8.8202804E-03 1.4873594E-02 1,midg,midg; igrid,midg,midg -1.4276640E-02 -7.5936411E-03 gauss-seidel spectral radius is 0.9982792 estimated iterations to convergence 191 setup time was (sec) 0.8400000 now iterating at: 17:27:22 rms-change max change #iterations 3.774722 154.6633 at 10iterations 1.610440 59.17924 at 20iterations 0.6877227 23.22187 at 30iterations 0.2945217 9.218834 at 40iterations 0.1252361 4.358992 at 50iterations 5.3539902E-02 1.778244 at 60iterations 2.2901662E-02 0.8247681 at 70iterations 9.8317415E-03 0.3316727 at 80iterations 4.2292164E-03 0.1359198 at 90iterations 1.8247452E-03 6.4533234E-02 at 100iterations 8.0018031E-04 2.7656555E-02 at 110iterations 3.6148197E-04 1.3516426E-02 at 120iterations finished qdiffx linear iterations at : 17:27:28 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.6148197E-04 1.3516426E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 17:27:29 6.997u 0.195s 0:07.48 95.9% 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 17:27:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.480913 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 2.480913 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271986 assigned positive charge : 525.4031 centred at (gu) : 90.66788 90.18407 87.61623 assigned negative charge : -530.6769 centred at (gu) : 90.79320 90.15175 87.48358 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86345 mr = 128887 m= 26677 mr = 69385 m= 4575 mr = 20439 m= 365 mr = 3015 m= 8 mr = 170 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1085 time to turn everything in is 1.360000 number of dielectric boundary points 72160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 26553 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) : 1.653942 object centre at (A) : 65.71300 48.39750 1.662000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1413433E-02 -3.9866108E-02 midg,1,midg; midg,igrid,midg 0.2759136 0.4944723 1,midg,midg; igrid,midg,midg -0.2283826 -8.1761822E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.680000 now iterating at: 17:27:31 rms-change max change #iterations 9.680768 300.4495 at 10iterations 5.494077 118.7303 at 20iterations 3.108973 72.17699 at 30iterations 1.755653 35.73637 at 40iterations 0.9862030 21.12379 at 50iterations 0.5525634 10.69891 at 60iterations 0.3090258 6.259631 at 70iterations 0.1728658 3.211256 at 80iterations 9.6435614E-02 1.786270 at 90iterations 5.3814378E-02 1.001003 at 100iterations 3.0022547E-02 0.5641747 at 110iterations 1.6768126E-02 0.3109217 at 120iterations 9.3695372E-03 0.1749992 at 130iterations 5.2238973E-03 0.1061983 at 140iterations 2.9268200E-03 5.5456161E-02 at 150iterations 1.6461299E-03 3.4523010E-02 at 160iterations 9.3255012E-04 1.9157410E-02 at 170iterations 5.3827255E-04 1.0330200E-02 at 180iterations finished qdiffx linear iterations at : 17:27:42 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 5.3827255E-04 1.0330200E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 17:27:42 13.163u 0.255s 0:13.68 98.0% 0+0k 0+0io 0pf+0w