Tue Oct 11 04:21:37 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 Tue Oct 11 2011 at 04:21:37 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 71 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6679049 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): -11.15200 36.79400 ymin,ymax (A): 7.001000 55.89500 zmin,zma (A): -7.774000 45.52700 x,y,z range (A): 47.94600 48.89400 53.30100 scale (grids/A): 0.6679049 object centre (A): 12.82100 31.44800 18.87650 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.514013 assigned positive charge : 410.5659 centred at (gu) : 90.14230 90.43296 91.34898 assigned negative charge : -405.0524 centred at (gu) : 89.87484 90.26437 91.38804 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8142 nv = 96 ne = 84 npr = 54544 no. pairs analyzed = 54544 no. exposed pairs = 3263 no. arc points = 23120 no. surface atoms = 1101 nbur = 1600 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 4618 m= 5 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0634827E-08 9.4579526E-09 midg,1,midg; midg,igrid,midg -2.3619480E-08 6.4509614E-08 1,midg,midg; igrid,midg,midg -5.0458784E-08 8.5241439E-08 gauss-seidel spectral radius is 0.9883901 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 04:21:38 rms-change max change #iterations 0.1781728 22.76789 at 10iterations 1.9790486E-02 2.627365 at 20iterations 2.1606043E-03 0.2768669 at 30iterations 2.5544758E-04 3.8124084E-02 at 40iterations 3.4934321E-05 4.5175552E-03 at 50iterations finished qdiffx linear iterations at : 04:21:40 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 3.4934321E-05 4.5175552E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 04:21:41 3.082u 0.151s 0:03.54 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 Tue Oct 11 2011 at 04:21:41 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 71 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.003715 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): -11.15200 36.79400 ymin,ymax (A): 7.001000 55.89500 zmin,zma (A): -7.774000 45.52700 x,y,z range (A): 47.94600 48.89400 53.30100 scale (grids/A): 2.003715 object centre (A): 12.82100 31.44800 18.87650 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.514013 assigned positive charge : 410.5659 centred at (gu) : 90.42628 91.29838 94.04639 assigned negative charge : -405.0524 centred at (gu) : 89.62427 90.79292 94.16402 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 87045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23120 grid for indexing accessible points = 1.400000 m= 35117 mr = 61266 m= 6832 mr = 26942 m= 528 mr = 4731 m= 8 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20137 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) : 0.6679049 object centre at (A) : 12.82100 31.44800 18.87650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3058565E-02 -2.1863428E-03 midg,1,midg; midg,igrid,midg -1.4530539E-02 3.8008083E-02 1,midg,midg; igrid,midg,midg -1.7071318E-02 7.4074261E-02 gauss-seidel spectral radius is 0.9987737 estimated iterations to convergence 226 setup time was (sec) 0.8600000 now iterating at: 04:21:42 rms-change max change #iterations 4.804392 234.8049 at 10iterations 2.351789 102.2806 at 20iterations 1.144816 34.45178 at 30iterations 0.5602277 15.60761 at 40iterations 0.2739233 8.119112 at 50iterations 0.1337538 3.706398 at 60iterations 6.5016471E-02 1.827576 at 70iterations 3.1861838E-02 0.8987470 at 80iterations 1.5513806E-02 0.4881229 at 90iterations 7.6120985E-03 0.2250447 at 100iterations 3.7095451E-03 0.1048660 at 110iterations 1.8140425E-03 4.9873352E-02 at 120iterations finished qdiffx linear iterations at : 04:21:48 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.8140425E-03 4.9873352E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 04:21:49 7.730u 0.173s 0:08.46 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 Tue Oct 11 2011 at 04:21:49 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 71 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 3.005572 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): -11.15200 36.79400 ymin,ymax (A): 7.001000 55.89500 zmin,zma (A): -7.774000 45.52700 x,y,z range (A): 47.94600 48.89400 53.30100 scale (grids/A): 3.005572 object centre (A): 12.82100 31.44800 18.87650 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.514013 assigned positive charge : 410.5659 centred at (gu) : 90.63924 91.94744 96.06940 assigned negative charge : -405.0524 centred at (gu) : 89.43644 91.18919 96.24596 start vw surface at 0.2300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 200251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23120 grid for indexing accessible points = 1.400000 m= 108892 mr = 147441 m= 45446 mr = 90759 m= 12858 mr = 37902 m= 2349 mr = 10171 m= 199 mr = 1707 m= 6 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 81919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 20384 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) : 2.003715 object centre at (A) : 12.82100 31.44800 18.87650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1187811 -6.7572489E-02 midg,1,midg; midg,igrid,midg -0.1660901 0.4206268 1,midg,midg; igrid,midg,midg -0.1085451 0.5548984 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.940000 now iterating at: 04:21:51 rms-change max change #iterations 11.04173 376.3019 at 10iterations 6.486996 134.7883 at 20iterations 3.815915 71.27300 at 30iterations 2.237280 44.56490 at 40iterations 1.312962 22.55413 at 50iterations 0.7680286 15.35199 at 60iterations 0.4486514 7.462217 at 70iterations 0.2621396 4.503382 at 80iterations 0.1533571 2.544323 at 90iterations 8.9474559E-02 1.542000 at 100iterations 5.2266374E-02 0.8619385 at 110iterations 3.0491814E-02 0.6084013 at 120iterations 1.7802183E-02 0.2906189 at 130iterations 1.0417325E-02 0.1676512 at 140iterations 6.0978816E-03 0.1016674 at 150iterations 3.5834273E-03 6.3051224E-02 at 160iterations 2.1172855E-03 3.4889221E-02 at 170iterations 1.2639369E-03 2.3231506E-02 at 180iterations finished qdiffx linear iterations at : 04:22:01 total time elapsed so far: 11.32000 # loops : 180 mean,max change (kT/e) : 1.2639369E-03 2.3231506E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 04:22:01 11.501u 0.182s 0:12.04 97.0% 0+0k 0+0io 0pf+0w