Mon Oct 10 11:05:30 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 Mon Oct 10 2011 at 11:05:30 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 = 5383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5211383 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): -46.13500 22.02400 ymin,ymax (A): -26.46800 41.84400 zmin,zma (A): 10.25700 72.37300 x,y,z range (A): 68.15900 68.31200 62.11600 scale (grids/A): 0.5211383 object centre (A): -12.05550 7.687999 41.31500 number of atom coordinates read : 5383 total number of charged atoms : 5228 net assigned charge : 11.00003 assigned positive charge : 854.4894 centred at (gu) : 89.28130 89.62610 88.13239 assigned negative charge : -843.4980 centred at (gu) : 89.27020 89.67673 88.11838 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9461 nv = 96 ne = 84 npr = 106241 no. pairs analyzed = 106241 no. exposed pairs = 6525 no. arc points = 44189 no. surface atoms = 2187 nbur = 3196 mkacc time = 0.2500000 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= 327 mr = 5221 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4501 ## 619 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12573 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8754712E-10 1.9615660E-10 midg,1,midg; midg,igrid,midg 5.3448934E-10 5.8585415E-12 1,midg,midg; igrid,midg,midg 2.3242488E-10 2.4991118E-10 gauss-seidel spectral radius is 0.9812052 estimated iterations to convergence 60 setup time was (sec) 0.7400000 now iterating at: 11:05:31 rms-change max change #iterations 8.2631461E-02 12.03353 at 10iterations 5.0030961E-03 0.7803631 at 20iterations 5.9791357E-04 8.4712982E-02 at 30iterations 2.5377196E-04 3.7250131E-02 at 40iterations 1.3216480E-04 1.9336522E-02 at 50iterations finished qdiffx linear iterations at : 11:05:34 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.3216480E-04 1.9336522E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:05:34 3.740u 0.205s 0:04.31 91.4% 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 Mon Oct 10 2011 at 11:05:34 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 = 5383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.563415 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): -46.13500 22.02400 ymin,ymax (A): -26.46800 41.84400 zmin,zma (A): 10.25700 72.37300 x,y,z range (A): 68.15900 68.31200 62.11600 scale (grids/A): 1.563415 object centre (A): -12.05550 7.687999 41.31500 number of atom coordinates read : 5383 total number of charged atoms : 5228 net assigned charge : 11.00003 assigned positive charge : 854.4894 centred at (gu) : 87.84197 88.87672 84.39536 assigned negative charge : -843.4980 centred at (gu) : 87.81080 89.03035 84.35497 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 107370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 33136 mr = 76830 m= 2984 mr = 22995 m= 63 mr = 1320 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1851 time to turn everything in is 0.7800000 number of dielectric boundary points 42408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 39437 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) : 0.5211383 object centre at (A) : -12.05550 7.687999 41.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5917614E-04 5.6799864E-03 midg,1,midg; midg,igrid,midg 1.9525107E-02 -3.5963353E-02 1,midg,midg; igrid,midg,midg 1.4137097E-03 2.1564720E-02 gauss-seidel spectral radius is 0.9982370 estimated iterations to convergence 189 setup time was (sec) 1.090000 now iterating at: 11:05:36 rms-change max change #iterations 4.351962 168.7793 at 10iterations 1.839870 58.30840 at 20iterations 0.7791038 21.99826 at 30iterations 0.3290146 9.415573 at 40iterations 0.1393360 4.054788 at 50iterations 5.8890410E-02 1.687893 at 60iterations 2.4966164E-02 0.7224426 at 70iterations 1.0631925E-02 0.3149433 at 80iterations 4.5517790E-03 0.1442940 at 90iterations 1.9838179E-03 5.6087494E-02 at 100iterations 9.1939478E-04 3.6172867E-02 at 110iterations 4.9072836E-04 1.8291473E-02 at 120iterations finished qdiffx linear iterations at : 11:05:43 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 4.9072836E-04 1.8291473E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 11:05:43 8.403u 0.219s 0:08.88 96.9% 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 Mon Oct 10 2011 at 11:05:43 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 = 5383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.345123 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): -46.13500 22.02400 ymin,ymax (A): -26.46800 41.84400 zmin,zma (A): 10.25700 72.37300 x,y,z range (A): 68.15900 68.31200 62.11600 scale (grids/A): 2.345123 object centre (A): -12.05550 7.687999 41.31500 number of atom coordinates read : 5383 total number of charged atoms : 5228 net assigned charge : 11.00003 assigned positive charge : 854.4894 centred at (gu) : 86.76292 88.31452 81.59252 assigned negative charge : -843.4980 centred at (gu) : 86.71623 88.54558 81.53249 start vw surface at 0.2100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 250425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 118089 mr = 188011 m= 31116 mr = 94526 m= 4358 mr = 23017 m= 211 mr = 2630 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 6363 time to turn everything in is 1.980000 number of dielectric boundary points 95936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 41727 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) : 1.563415 object centre at (A) : -12.05550 7.687999 41.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1249461 7.2165765E-02 midg,1,midg; midg,igrid,midg 0.4150357 -0.9728678 1,midg,midg; igrid,midg,midg -9.5864750E-02 0.3669094 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 2.350000 now iterating at: 11:05:46 rms-change max change #iterations 11.54147 282.0107 at 10iterations 6.680608 140.9854 at 20iterations 3.831961 96.39940 at 30iterations 2.192040 46.27397 at 40iterations 1.249633 23.13115 at 50iterations 0.7093985 12.42148 at 60iterations 0.4015495 7.175019 at 70iterations 0.2276992 4.235870 at 80iterations 0.1287162 2.138607 at 90iterations 7.2568290E-02 1.269896 at 100iterations 4.0951703E-02 0.6977997 at 110iterations 2.3147263E-02 0.4624586 at 120iterations 1.3029731E-02 0.2320633 at 130iterations 7.3501808E-03 0.1431930 at 140iterations 4.1485582E-03 7.1723938E-02 at 150iterations 2.3466100E-03 4.2436600E-02 at 160iterations 1.3415000E-03 2.6142120E-02 at 170iterations 7.7702699E-04 1.5433311E-02 at 180iterations finished qdiffx linear iterations at : 11:05:57 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 7.7702699E-04 1.5433311E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 11:05:57 13.745u 0.248s 0:14.27 97.9% 0+0k 0+0io 0pf+0w