Sat Oct 15 15:26:28 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 15:26:29 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: HIR 70 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6414877 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): -12.41300 37.29000 ymin,ymax (A): -25.73700 22.49900 zmin,zma (A): -10.17200 45.32400 x,y,z range (A): 49.70300 48.23600 55.49600 scale (grids/A): 0.6414877 object centre (A): 12.43850 -1.618999 17.57600 number of atom coordinates read : 2718 total number of charged atoms : 2570 net assigned charge : 3.514013 assigned positive charge : 416.5238 centred at (gu) : 90.22534 90.42940 92.00021 assigned negative charge : -413.0103 centred at (gu) : 89.99864 90.23811 91.94141 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7386 nv = 96 ne = 84 npr = 55883 no. pairs analyzed = 55883 no. exposed pairs = 3382 no. arc points = 23346 no. surface atoms = 1131 nbur = 1587 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4153 m= 5 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2100000 number of dielectric boundary points 3609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2342 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6102282E-09 1.9297620E-08 midg,1,midg; midg,igrid,midg -1.8311628E-08 3.1973912E-08 1,midg,midg; igrid,midg,midg -2.3696503E-08 3.5168046E-08 gauss-seidel spectral radius is 0.9874152 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 15:26:29 rms-change max change #iterations 0.1555350 23.00790 at 10iterations 1.5656617E-02 2.020808 at 20iterations 1.6124652E-03 0.2272310 at 30iterations 1.7481626E-04 2.6556015E-02 at 40iterations 2.3627681E-05 4.3907166E-03 at 50iterations finished qdiffx linear iterations at : 15:26:34 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.3627681E-05 4.3907166E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 15:26:34 3.575u 0.190s 0:05.45 68.9% 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 Sat Oct 15 2011 at 15:26:34 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: HIR 70 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.924463 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): -12.41300 37.29000 ymin,ymax (A): -25.73700 22.49900 zmin,zma (A): -10.17200 45.32400 x,y,z range (A): 49.70300 48.23600 55.49600 scale (grids/A): 1.924463 object centre (A): 12.43850 -1.618999 17.57600 number of atom coordinates read : 2718 total number of charged atoms : 2570 net assigned charge : 3.514013 assigned positive charge : 416.5238 centred at (gu) : 90.67548 91.28779 96.00031 assigned negative charge : -413.0103 centred at (gu) : 89.99545 90.71401 95.82395 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23346 grid for indexing accessible points = 1.400000 m= 28398 mr = 55504 m= 4134 mr = 20892 m= 192 mr = 2467 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1285 time to turn everything in is 0.4000000 number of dielectric boundary points 33294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20261 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) : 0.6414877 object centre at (A) : 12.43850 -1.618999 17.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8865758E-02 1.8419821E-02 midg,1,midg; midg,igrid,midg -1.5362921E-02 2.4630869E-02 1,midg,midg; igrid,midg,midg -5.2719666E-03 5.4972831E-02 gauss-seidel spectral radius is 0.9986723 estimated iterations to convergence 217 setup time was (sec) 0.6300000 now iterating at: 15:26:35 rms-change max change #iterations 4.530112 177.9117 at 10iterations 2.135960 72.34765 at 20iterations 1.016107 32.38171 at 30iterations 0.4815808 15.78081 at 40iterations 0.2278438 7.113491 at 50iterations 0.1084351 3.299538 at 60iterations 5.1294070E-02 1.535345 at 70iterations 2.4299139E-02 0.7058105 at 80iterations 1.1529313E-02 0.3455753 at 90iterations 5.4861377E-03 0.1671200 at 100iterations 2.5970840E-03 8.3887100E-02 at 110iterations 1.2361526E-03 3.7431717E-02 at 120iterations finished qdiffx linear iterations at : 15:26:42 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 1.2361526E-03 3.7431717E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 15:26:43 8.271u 0.225s 0:09.07 93.6% 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 15:26:43 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: HIR 70 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.886694 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): -12.41300 37.29000 ymin,ymax (A): -25.73700 22.49900 zmin,zma (A): -10.17200 45.32400 x,y,z range (A): 49.70300 48.23600 55.49600 scale (grids/A): 2.886694 object centre (A): 12.43850 -1.618999 17.57600 number of atom coordinates read : 2718 total number of charged atoms : 2570 net assigned charge : 3.514013 assigned positive charge : 416.5238 centred at (gu) : 91.01320 91.93166 99.00010 assigned negative charge : -413.0103 centred at (gu) : 89.99298 91.07081 98.73585 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23346 grid for indexing accessible points = 1.400000 m= 93115 mr = 134148 m= 32669 mr = 76264 m= 7223 mr = 26233 m= 847 mr = 5202 m= 34 mr = 509 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 4364 time to turn everything in is 1.070000 number of dielectric boundary points 75175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20559 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) : 1.924463 object centre at (A) : 12.43850 -1.618999 17.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4363636 0.4059434 midg,1,midg; midg,igrid,midg -0.1613686 0.2729643 1,midg,midg; igrid,midg,midg -1.7417137E-02 0.4788518 gauss-seidel spectral radius is 0.9992676 estimated iterations to convergence 292 setup time was (sec) 1.340000 now iterating at: 15:26:45 rms-change max change #iterations 10.51800 364.7301 at 10iterations 6.152078 163.8408 at 20iterations 3.589360 76.82344 at 30iterations 2.089034 41.70299 at 40iterations 1.211980 24.17637 at 50iterations 0.7030151 14.05063 at 60iterations 0.4079382 7.161302 at 70iterations 0.2359062 4.168983 at 80iterations 0.1363627 2.486323 at 90iterations 7.8799911E-02 1.655126 at 100iterations 4.5571741E-02 0.8150010 at 110iterations 2.6355831E-02 0.5017662 at 120iterations 1.5220733E-02 0.2719688 at 130iterations 8.7984102E-03 0.1540451 at 140iterations 5.0749136E-03 8.9373589E-02 at 150iterations 2.9485943E-03 5.3648472E-02 at 160iterations 1.7080385E-03 3.0097961E-02 at 170iterations 9.9351071E-04 1.8768311E-02 at 180iterations finished qdiffx linear iterations at : 15:26:57 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 9.9351071E-04 1.8768311E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 15:26:58 13.899u 0.257s 0:14.80 95.5% 0+0k 0+0io 0pf+0w