Sat Oct 15 13:43:57 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 15 2011 at 13:43:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: HIQ 142 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4817647 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 0.4817647 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.98598 assigned positive charge : 520.2639 centred at (gu) : 88.72274 88.92046 88.59325 assigned negative charge : -538.2517 centred at (gu) : 88.78310 88.86493 88.59178 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5147 nv = 96 ne = 84 npr = 63491 no. pairs analyzed = 63491 no. exposed pairs = 5068 no. arc points = 36708 no. surface atoms = 1672 nbur = 1730 mkacc time = 0.1100000 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 = 1.764000 m= 176 mr = 2183 m= 0 mr = 3 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3437 ## 634 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6642937E-11 -4.4078768E-11 midg,1,midg; midg,igrid,midg -1.2731294E-10 -2.7244831E-11 1,midg,midg; igrid,midg,midg -4.6877158E-11 -6.8557340E-11 gauss-seidel spectral radius is 0.9779100 estimated iterations to convergence 56 setup time was (sec) 0.4400000 now iterating at: 13:43:58 rms-change max change #iterations 4.1580327E-02 9.516411 at 10iterations 2.2923108E-03 0.4539413 at 20iterations 3.0025272E-04 8.8939667E-02 at 30iterations 6.8292604E-05 2.1429062E-02 at 40iterations 1.6212392E-05 5.2051544E-03 at 50iterations finished qdiffx linear iterations at : 13:44:01 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.6212392E-05 5.2051544E-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) 3.590000 DelPhi exited at 13:44:01 3.595u 0.173s 0:04.25 88.4% 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 15 2011 at 13:44:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: HIQ 142 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.445294 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 1.445294 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.98598 assigned positive charge : 520.2639 centred at (gu) : 86.16729 86.76044 85.77859 assigned negative charge : -538.2517 centred at (gu) : 86.34888 86.59464 85.77477 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 13907 mr = 34878 m= 956 mr = 7910 m= 9 mr = 278 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.3000000 number of dielectric boundary points 29659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 570 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 23849 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) : 0.4817647 object centre at (A) : -0.9190006 -27.04400 -49.59450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1924889E-03 -1.0650949E-02 midg,1,midg; midg,igrid,midg -1.0621930E-02 -3.0009819E-03 1,midg,midg; igrid,midg,midg -8.8847545E-04 -6.1149034E-03 gauss-seidel spectral radius is 0.9977219 estimated iterations to convergence 167 setup time was (sec) 0.5200000 now iterating at: 13:44:02 rms-change max change #iterations 2.761900 139.0523 at 10iterations 1.034678 54.22166 at 20iterations 0.3852980 16.91021 at 30iterations 0.1437306 5.872518 at 40iterations 5.4149665E-02 2.167770 at 50iterations 2.0195706E-02 0.8578825 at 60iterations 7.6740826E-03 0.3200626 at 70iterations 2.9333543E-03 0.1321068 at 80iterations 1.1536259E-03 5.6159973E-02 at 90iterations 4.8224640E-04 2.5547028E-02 at 100iterations 2.2241002E-04 1.2438774E-02 at 110iterations 1.1472557E-04 7.0075989E-03 at 120iterations finished qdiffx linear iterations at : 13:44:11 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.1472557E-04 7.0075989E-03 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 13:44:12 8.017u 0.238s 0:10.74 76.7% 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 Sat Oct 15 2011 at 13:44:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: HIQ 142 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.167941 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 2.167941 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.98598 assigned positive charge : 520.2639 centred at (gu) : 84.25070 85.14011 83.66759 assigned negative charge : -538.2517 centred at (gu) : 84.52332 84.89177 83.66206 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 135049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 51625 mr = 87477 m= 10926 mr = 36728 m= 1193 mr = 6939 m= 39 mr = 593 m= 0 mr = 4 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 276 time to turn everything in is 0.6900000 number of dielectric boundary points 67091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25760 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) : 1.445294 object centre at (A) : -0.9190006 -27.04400 -49.59450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0323679E-02 -0.2706501 midg,1,midg; midg,igrid,midg -0.1923776 -5.5374306E-02 1,midg,midg; igrid,midg,midg 4.3385206E-03 -0.1232204 gauss-seidel spectral radius is 0.9989942 estimated iterations to convergence 249 setup time was (sec) 0.9500000 now iterating at: 13:44:13 rms-change max change #iterations 7.869627 306.7058 at 10iterations 4.245760 132.2749 at 20iterations 2.272236 62.78524 at 30iterations 1.210738 36.19820 at 40iterations 0.6439314 18.20459 at 50iterations 0.3389798 9.766205 at 60iterations 0.1792184 4.355272 at 70iterations 9.4563589E-02 2.442986 at 80iterations 4.9797732E-02 1.179864 at 90iterations 2.6189780E-02 0.6183785 at 100iterations 1.3693232E-02 0.3285885 at 110iterations 7.1826288E-03 0.1961098 at 120iterations 3.7757005E-03 8.6031199E-02 at 130iterations 1.9845886E-03 4.6916962E-02 at 140iterations 1.0430348E-03 2.8123856E-02 at 150iterations 5.5124058E-04 1.3537884E-02 at 160iterations 2.9299353E-04 7.6293945E-03 at 170iterations 1.5797572E-04 3.9920807E-03 at 180iterations finished qdiffx linear iterations at : 13:44:25 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 1.5797572E-04 3.9920807E-03 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 13:44:26 13.348u 0.272s 0:13.98 97.3% 0+0k 0+0io 0pf+0w