Mon Oct 10 11:45:46 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 Mon Oct 10 2011 at 11:45:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 0.7406329 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 0.7406329 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 88.92089 89.88747 89.97523 assigned negative charge : -320.2120 centred at (gu) : 88.93271 89.94727 90.11708 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7951 nv = 96 ne = 84 npr = 43473 no. pairs analyzed = 43473 no. exposed pairs = 2633 no. arc points = 19024 no. surface atoms = 892 nbur = 1213 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4423 m= 6 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.2800000 number of dielectric boundary points 3954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1572 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4861843E-08 -2.3625572E-07 midg,1,midg; midg,igrid,midg -2.8719612E-08 -1.4817140E-07 1,midg,midg; igrid,midg,midg -9.3744809E-08 -8.3623526E-08 gauss-seidel spectral radius is 0.9904990 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 11:45:46 rms-change max change #iterations 0.2480232 35.85410 at 10iterations 3.3651523E-02 4.233237 at 20iterations 4.5799683E-03 0.5582886 at 30iterations 6.0774054E-04 8.5146904E-02 at 40iterations 8.1499806E-05 9.8466873E-03 at 50iterations finished qdiffx linear iterations at : 11:45:49 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 8.1499806E-05 9.8466873E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 11:45:49 3.324u 0.144s 0:03.81 90.8% 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 11:45:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 2.221899 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 2.221899 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 86.76264 89.66223 89.92566 assigned negative charge : -320.2120 centred at (gu) : 86.79800 89.84183 90.35134 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 83304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19024 grid for indexing accessible points = 1.400000 m= 33384 mr = 57466 m= 7433 mr = 25584 m= 840 mr = 5189 m= 33 mr = 503 m= 0 mr = 11 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2467 time to turn everything in is 0.6400000 number of dielectric boundary points 36241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15678 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) : 0.7406329 object centre at (A) : 1.689500 14.77600 20.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1973860E-03 -0.1173185 midg,1,midg; midg,igrid,midg -2.4541678E-02 -3.3249248E-02 1,midg,midg; igrid,midg,midg -2.3174666E-02 -2.7151331E-03 gauss-seidel spectral radius is 0.9989262 estimated iterations to convergence 241 setup time was (sec) 0.9300000 now iterating at: 11:45:51 rms-change max change #iterations 5.077322 214.4774 at 10iterations 2.576795 89.72644 at 20iterations 1.309990 36.55720 at 30iterations 0.6686181 21.74706 at 40iterations 0.3402143 9.462124 at 50iterations 0.1732258 5.299114 at 60iterations 8.8633545E-02 2.387694 at 70iterations 4.5062240E-02 1.245846 at 80iterations 2.3030022E-02 0.6625671 at 90iterations 1.1713969E-02 0.3494492 at 100iterations 5.9887879E-03 0.2014637 at 110iterations 3.0439780E-03 8.6420059E-02 at 120iterations finished qdiffx linear iterations at : 11:45:57 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 3.0439780E-03 8.6420059E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 11:45:58 7.631u 0.180s 0:08.37 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 Mon Oct 10 2011 at 11:45:58 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 3.332848 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 3.332848 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 85.14400 89.49336 89.88850 assigned negative charge : -320.2120 centred at (gu) : 85.19691 89.76273 90.52701 start vw surface at 0.1400000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 191793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19024 grid for indexing accessible points = 1.400000 m= 102160 mr = 138286 m= 44038 mr = 85045 m= 14312 mr = 36596 m= 3461 mr = 11552 m= 563 mr = 2688 m= 40 mr = 423 m= 0 mr = 17 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 8011 time to turn everything in is 2.080000 number of dielectric boundary points 81760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 15736 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) : 2.221899 object centre at (A) : 1.689500 14.77600 20.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7014828E-02 -1.308203 midg,1,midg; midg,igrid,midg -0.2349612 -0.1734674 1,midg,midg; igrid,midg,midg -0.2924446 -8.8048205E-02 gauss-seidel spectral radius is 0.9993178 estimated iterations to convergence 302 setup time was (sec) 2.370000 now iterating at: 11:46:00 rms-change max change #iterations 10.93712 324.6100 at 10iterations 6.453889 123.0182 at 20iterations 3.806184 74.34578 at 30iterations 2.240525 37.67373 at 40iterations 1.317611 22.23366 at 50iterations 0.7766665 12.91874 at 60iterations 0.4559732 8.153777 at 70iterations 0.2684233 4.545335 at 80iterations 0.1575055 2.588148 at 90iterations 9.2502296E-02 1.499733 at 100iterations 5.4360859E-02 0.8362389 at 110iterations 3.1908102E-02 0.5223632 at 120iterations 1.8741859E-02 0.3051870 at 130iterations 1.0993012E-02 0.1722717 at 140iterations 6.4446535E-03 9.7158432E-02 at 150iterations 3.7881751E-03 5.9917450E-02 at 160iterations 2.2217059E-03 3.7107468E-02 at 170iterations 1.3040706E-03 1.9747734E-02 at 180iterations finished qdiffx linear iterations at : 11:46:11 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.3040706E-03 1.9747734E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 11:46:11 12.769u 0.194s 0:13.30 97.3% 0+0k 0+0io 0pf+0w