Tue Oct 11 04:21:13 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 04:21:13 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-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 : 5.500012 assigned positive charge : 407.3239 centred at (gu) : 90.12237 90.47895 91.34019 assigned negative charge : -401.8244 centred at (gu) : 89.85636 90.31406 91.38084 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 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 = 0.1200000 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 = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 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 0.3900000 number of grid points assigned charge 9466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0877035E-08 8.9579695E-09 midg,1,midg; midg,igrid,midg -2.2243963E-08 6.3724286E-08 1,midg,midg; igrid,midg,midg -4.9803859E-08 8.3957097E-08 gauss-seidel spectral radius is 0.9883901 estimated iterations to convergence 76 setup time was (sec) 0.5000000 now iterating at: 04:21:14 rms-change max change #iterations 0.1756415 21.73014 at 10iterations 1.9563958E-02 2.457693 at 20iterations 2.1323457E-03 0.2772102 at 30iterations 2.5328246E-04 3.8200378E-02 at 40iterations 3.6365003E-05 4.6854019E-03 at 50iterations finished qdiffx linear iterations at : 04:21:16 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 3.6365003E-05 4.6854019E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 04:21:17 3.070u 0.149s 0:03.71 86.5% 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 04:21:17 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 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: 2.003715 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 : 5.500012 assigned positive charge : 407.3239 centred at (gu) : 90.36643 91.43633 94.01995 assigned negative charge : -401.8244 centred at (gu) : 89.56880 90.94210 94.14243 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 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 0.6500000 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 0.7600000 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 2.3190167E-02 -3.2011766E-03 midg,1,midg; midg,igrid,midg -1.3245435E-02 3.7703160E-02 1,midg,midg; igrid,midg,midg -1.7009940E-02 7.0914865E-02 gauss-seidel spectral radius is 0.9987737 estimated iterations to convergence 226 setup time was (sec) 0.9400000 now iterating at: 04:21:18 rms-change max change #iterations 4.755430 234.8049 at 10iterations 2.327127 102.2806 at 20iterations 1.133486 34.45184 at 30iterations 0.5545189 15.71222 at 40iterations 0.2712528 8.149317 at 50iterations 0.1324217 3.651947 at 60iterations 6.4351141E-02 1.854679 at 70iterations 3.1547852E-02 0.9098473 at 80iterations 1.5357179E-02 0.4732952 at 90iterations 7.5379759E-03 0.2265530 at 100iterations 3.6733814E-03 0.1003380 at 110iterations 1.7962443E-03 4.8523903E-02 at 120iterations finished qdiffx linear iterations at : 04:21:24 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 1.7962443E-03 4.8523903E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 04:21:25 7.285u 0.191s 0:07.95 93.9% 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 Tue Oct 11 2011 at 04:21:25 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 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: 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 : 5.500012 assigned positive charge : 407.3239 centred at (gu) : 90.54950 92.15434 96.02974 assigned negative charge : -401.8244 centred at (gu) : 89.35326 91.41295 96.21358 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 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 1.540000 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 1.670000 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 0.1197475 -8.0566004E-02 midg,1,midg; midg,igrid,midg -0.1627686 0.4179018 1,midg,midg; igrid,midg,midg -0.1087359 0.5237977 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.820000 now iterating at: 04:21:27 rms-change max change #iterations 10.92628 376.3019 at 10iterations 6.419130 134.8024 at 20iterations 3.776792 71.30615 at 30iterations 2.214740 44.70487 at 40iterations 1.300061 23.50751 at 50iterations 0.7607363 15.15504 at 60iterations 0.4444856 7.352959 at 70iterations 0.2597487 4.403218 at 80iterations 0.1519562 2.490377 at 90iterations 8.8673435E-02 1.535875 at 100iterations 5.1794332E-02 0.8730774 at 110iterations 3.0220659E-02 0.6004267 at 120iterations 1.7637858E-02 0.2902908 at 130iterations 1.0315979E-02 0.1660261 at 140iterations 6.0361316E-03 0.1039562 at 150iterations 3.5452547E-03 6.3903570E-02 at 160iterations 2.0917603E-03 3.5438538E-02 at 170iterations 1.2460573E-03 2.2853851E-02 at 180iterations finished qdiffx linear iterations at : 04:21:36 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 1.2460573E-03 2.2853851E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 04:21:37 11.378u 0.184s 0:11.90 97.0% 0+0k 0+0io 0pf+0w