Sat Oct 15 15:18:57 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 15:18:57 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6676794 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): -7.608000 40.91300 ymin,ymax (A): -25.93900 21.52300 zmin,zma (A): -9.838000 43.48100 x,y,z range (A): 48.52100 47.46200 53.31900 scale (grids/A): 0.6676794 object centre (A): 16.65250 -2.208000 16.82150 number of atom coordinates read : 2755 total number of charged atoms : 2607 net assigned charge : 1.970019 assigned positive charge : 421.2785 centred at (gu) : 89.70332 90.31102 88.56197 assigned negative charge : -419.3093 centred at (gu) : 89.91519 90.14321 88.65356 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8125 nv = 96 ne = 84 npr = 56354 no. pairs analyzed = 56354 no. exposed pairs = 3391 no. arc points = 23634 no. surface atoms = 1139 nbur = 1616 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4585 m= 8 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2200000 number of dielectric boundary points 3982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9276152E-08 -1.3588627E-08 midg,1,midg; midg,igrid,midg -3.6279232E-08 5.1527905E-08 1,midg,midg; igrid,midg,midg 6.3058970E-08 -4.7561375E-08 gauss-seidel spectral radius is 0.9883833 estimated iterations to convergence 76 setup time was (sec) 0.4700000 now iterating at: 15:18:58 rms-change max change #iterations 0.1863160 26.95703 at 10iterations 2.0286825E-02 2.540169 at 20iterations 2.2349313E-03 0.2869015 at 30iterations 2.4374491E-04 3.0830383E-02 at 40iterations 2.8073398E-05 4.0054321E-03 at 50iterations finished qdiffx linear iterations at : 15:19:01 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 2.8073398E-05 4.0054321E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 15:19:02 4.012u 0.223s 0:04.53 93.3% 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 15 2011 at 15:19:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.003038 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): -7.608000 40.91300 ymin,ymax (A): -25.93900 21.52300 zmin,zma (A): -9.838000 43.48100 x,y,z range (A): 48.52100 47.46200 53.31900 scale (grids/A): 2.003038 object centre (A): 16.65250 -2.208000 16.82150 number of atom coordinates read : 2755 total number of charged atoms : 2607 net assigned charge : 1.970019 assigned positive charge : 421.2785 centred at (gu) : 89.10937 90.93251 85.68511 assigned negative charge : -419.3093 centred at (gu) : 89.74519 90.42951 85.96049 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23634 grid for indexing accessible points = 1.400000 m= 34927 mr = 60046 m= 7035 mr = 26558 m= 574 mr = 4842 m= 5 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.4700000 number of dielectric boundary points 36850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 20634 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) : 0.6676794 object centre at (A) : 16.65250 -2.208000 16.82150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6748871E-03 -5.8297630E-02 midg,1,midg; midg,igrid,midg -2.4496946E-02 3.3151403E-02 1,midg,midg; igrid,midg,midg 7.9909757E-02 -7.3012877E-03 gauss-seidel spectral radius is 0.9987755 estimated iterations to convergence 226 setup time was (sec) 0.7400000 now iterating at: 15:19:03 rms-change max change #iterations 4.937948 304.3507 at 10iterations 2.402645 76.57879 at 20iterations 1.177114 37.47452 at 30iterations 0.5750079 17.12471 at 40iterations 0.2811437 9.190818 at 50iterations 0.1374259 3.905216 at 60iterations 6.7157775E-02 1.975960 at 70iterations 3.2702304E-02 0.8746033 at 80iterations 1.6042657E-02 0.4760780 at 90iterations 7.8260750E-03 0.2209015 at 100iterations 3.8323200E-03 0.1261206 at 110iterations 1.8749936E-03 5.4953575E-02 at 120iterations finished qdiffx linear iterations at : 15:19:12 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 1.8749936E-03 5.4953575E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 15:19:12 9.760u 0.282s 0:10.39 96.6% 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 15:19:12 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.004557 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): -7.608000 40.91300 ymin,ymax (A): -25.93900 21.52300 zmin,zma (A): -9.838000 43.48100 x,y,z range (A): 48.52100 47.46200 53.31900 scale (grids/A): 3.004557 object centre (A): 16.65250 -2.208000 16.82150 number of atom coordinates read : 2755 total number of charged atoms : 2607 net assigned charge : 1.970019 assigned positive charge : 421.2785 centred at (gu) : 88.66371 91.39852 83.52755 assigned negative charge : -419.3093 centred at (gu) : 89.61788 90.64422 83.94069 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 198358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23634 grid for indexing accessible points = 1.400000 m= 107330 mr = 144899 m= 45339 mr = 89043 m= 13313 mr = 37502 m= 2468 mr = 10431 m= 166 mr = 1781 m= 5 mr = 68 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1499 time to turn everything in is 1.250000 number of dielectric boundary points 83256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 20848 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) : 2.003038 object centre at (A) : 16.65250 -2.208000 16.82150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2164870 -0.7541554 midg,1,midg; midg,igrid,midg -0.2985557 0.3918647 1,midg,midg; igrid,midg,midg 0.6791627 -3.8942199E-02 gauss-seidel spectral radius is 0.9992943 estimated iterations to convergence 297 setup time was (sec) 1.550000 now iterating at: 15:19:14 rms-change max change #iterations 11.21974 404.9318 at 10iterations 6.618975 151.4282 at 20iterations 3.890605 82.45162 at 30iterations 2.286546 41.30075 at 40iterations 1.340662 23.15991 at 50iterations 0.7864552 14.30395 at 60iterations 0.4593560 8.081929 at 70iterations 0.2685701 4.566666 at 80iterations 0.1570041 2.621237 at 90iterations 9.1784805E-02 1.596233 at 100iterations 5.3550519E-02 0.9230576 at 110iterations 3.1205058E-02 0.5129349 at 120iterations 1.8237099E-02 0.3005042 at 130iterations 1.0616566E-02 0.1690903 at 140iterations 6.2025031E-03 0.1043959 at 150iterations 3.6189363E-03 6.3169479E-02 at 160iterations 2.1200876E-03 3.6894798E-02 at 170iterations 1.2388545E-03 2.2472382E-02 at 180iterations finished qdiffx linear iterations at : 15:19:28 total time elapsed so far: 15.49000 # loops : 180 mean,max change (kT/e) : 1.2388545E-03 2.2472382E-02 energy calculations done at 15.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.61000 DelPhi exited at 15:19:29 15.610u 0.328s 0:16.30 97.7% 0+0k 0+0io 0pf+0w