Tue Oct 11 08:30:16 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 Tue Oct 11 2011 at 08:30:16 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 = 3979 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5288804 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 0.5288804 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3820 net assigned charge : 10.00002 assigned positive charge : 610.9174 centred at (gu) : 89.62991 89.99379 93.25912 assigned negative charge : -600.9213 centred at (gu) : 89.69470 89.94996 93.35994 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7162 nv = 96 ne = 84 npr = 77137 no. pairs analyzed = 77137 no. exposed pairs = 5516 no. arc points = 38988 no. surface atoms = 1821 nbur = 2158 mkacc time = 0.2100000 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 = 1.624000 m= 244 mr = 3391 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3875 ## 563 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4527686E-10 -3.6783829E-10 midg,1,midg; midg,igrid,midg 1.2244208E-10 5.2213756E-10 1,midg,midg; igrid,midg,midg 6.7824146E-10 2.4008909E-11 gauss-seidel spectral radius is 0.9816604 estimated iterations to convergence 61 setup time was (sec) 0.7800000 now iterating at: 08:30:18 rms-change max change #iterations 7.1351916E-02 10.91794 at 10iterations 4.5752241E-03 0.7674732 at 20iterations 3.7061871E-04 5.2230835E-02 at 30iterations 6.3879634E-05 8.4781647E-03 at 40iterations 1.6061638E-05 1.9645691E-03 at 50iterations finished qdiffx linear iterations at : 08:30:22 total time elapsed so far: 5.400000 # loops : 50 mean,max change (kT/e) : 1.6061638E-05 1.9645691E-03 energy calculations done at 5.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.570000 DelPhi exited at 08:30:23 5.571u 0.391s 0:06.39 93.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 08:30:23 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 = 3979 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.586641 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 1.586641 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3820 net assigned charge : 10.00002 assigned positive charge : 610.9174 centred at (gu) : 88.88811 89.97960 99.77554 assigned negative charge : -600.9213 centred at (gu) : 89.08349 89.84961 100.0796 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22150 mr = 50907 m= 1890 mr = 13964 m= 38 mr = 727 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 434 time to turn everything in is 0.6700000 number of dielectric boundary points 37546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 28953 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) : 0.5288804 object centre at (A) : 17.69600 55.97850 46.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0893465E-02 9.0794591E-03 midg,1,midg; midg,igrid,midg 1.3898497E-02 1.5029471E-02 1,midg,midg; igrid,midg,midg 2.8079165E-02 9.7404933E-03 gauss-seidel spectral radius is 0.9981726 estimated iterations to convergence 186 setup time was (sec) 1.100000 now iterating at: 08:30:24 rms-change max change #iterations 3.693292 164.8775 at 10iterations 1.533620 58.36689 at 20iterations 0.6354395 22.75353 at 30iterations 0.2632532 9.101783 at 40iterations 0.1091311 3.628643 at 50iterations 4.5312636E-02 1.598431 at 60iterations 1.8910602E-02 0.5982761 at 70iterations 7.8710541E-03 0.2973518 at 80iterations 3.2882378E-03 0.1213799 at 90iterations 1.3789731E-03 4.3992996E-02 at 100iterations 5.8609404E-04 2.6065826E-02 at 110iterations 2.5274951E-04 8.9249611E-03 at 120iterations finished qdiffx linear iterations at : 08:30:37 total time elapsed so far: 13.66000 # loops : 120 mean,max change (kT/e) : 2.5274951E-04 8.9249611E-03 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 08:30:37 13.820u 0.509s 0:14.68 97.5% 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 Tue Oct 11 2011 at 08:30:38 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 = 3979 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.379962 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 2.379962 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3820 net assigned charge : 10.00002 assigned positive charge : 610.9174 centred at (gu) : 88.33167 89.96905 104.6631 assigned negative charge : -600.9213 centred at (gu) : 88.62500 89.77418 105.1193 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 183686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 79036 mr = 125899 m= 19756 mr = 59274 m= 2740 mr = 13686 m= 107 mr = 1580 m= 0 mr = 20 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1494 time to turn everything in is 1.660000 number of dielectric boundary points 84866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 30520 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) : 1.586641 object centre at (A) : 17.69600 55.97850 46.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1164366 0.1740774 midg,1,midg; midg,igrid,midg 0.2246849 0.2720797 1,midg,midg; igrid,midg,midg 0.3663799 9.6819378E-02 gauss-seidel spectral radius is 0.9991561 estimated iterations to convergence 272 setup time was (sec) 2.050000 now iterating at: 08:30:40 rms-change max change #iterations 9.873621 310.7336 at 10iterations 5.622376 144.9392 at 20iterations 3.181434 68.41331 at 30iterations 1.786341 43.67774 at 40iterations 1.000689 23.44621 at 50iterations 0.5589823 12.78237 at 60iterations 0.3112940 6.087740 at 70iterations 0.1732917 3.696409 at 80iterations 9.6140660E-02 1.982637 at 90iterations 5.3453214E-02 1.137268 at 100iterations 2.9607346E-02 0.6014214 at 110iterations 1.6413374E-02 0.3291855 at 120iterations 9.1027366E-03 0.1926007 at 130iterations 5.0435010E-03 9.9065781E-02 at 140iterations 2.7900154E-03 5.2902222E-02 at 150iterations 1.5517755E-03 3.2036781E-02 at 160iterations 8.6131110E-04 1.7133713E-02 at 170iterations 4.7975656E-04 9.7084045E-03 at 180iterations finished qdiffx linear iterations at : 08:31:01 total time elapsed so far: 23.10000 # loops : 180 mean,max change (kT/e) : 4.7975656E-04 9.7084045E-03 energy calculations done at 23.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.27000 DelPhi exited at 08:31:02 23.271u 0.559s 0:24.19 98.4% 0+0k 0+0io 0pf+0w