Sat Oct 15 12:55:27 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 Sat Oct 15 2011 at 12:55:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6753296 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): -4.843000 44.21700 ymin,ymax (A): -13.95100 38.76400 zmin,zma (A): -0.5230000 44.57600 x,y,z range (A): 49.06000 52.71500 45.09900 scale (grids/A): 0.6753296 object centre (A): 19.68700 12.40650 22.02650 number of atom coordinates read : 2393 total number of charged atoms : 2252 net assigned charge : 4.500014 assigned positive charge : 365.3330 centred at (gu) : 88.91782 90.53654 91.19717 assigned negative charge : -360.8336 centred at (gu) : 88.95688 90.64958 91.27107 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7236 nv = 96 ne = 84 npr = 48675 no. pairs analyzed = 48675 no. exposed pairs = 2973 no. arc points = 20798 no. surface atoms = 1000 nbur = 1393 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3987 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9248124E-08 -3.6430949E-09 midg,1,midg; midg,igrid,midg 4.2634738E-08 -1.5035109E-08 1,midg,midg; igrid,midg,midg 3.4769723E-08 5.6974456E-09 gauss-seidel spectral radius is 0.9886110 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 12:55:27 rms-change max change #iterations 0.1727690 24.02349 at 10iterations 1.9867223E-02 2.623500 at 20iterations 2.7426528E-03 0.3966446 at 30iterations 5.8539765E-04 9.6019745E-02 at 40iterations 1.7575176E-04 2.9914856E-02 at 50iterations finished qdiffx linear iterations at : 12:55:30 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.7575176E-04 2.9914856E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 12:55:31 3.482u 0.203s 0:04.15 88.6% 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 12:55:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 2.025989 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): -4.843000 44.21700 ymin,ymax (A): -13.95100 38.76400 zmin,zma (A): -0.5230000 44.57600 x,y,z range (A): 49.06000 52.71500 45.09900 scale (grids/A): 2.025989 object centre (A): 19.68700 12.40650 22.02650 number of atom coordinates read : 2393 total number of charged atoms : 2252 net assigned charge : 4.500014 assigned positive charge : 365.3330 centred at (gu) : 86.75309 91.60905 93.59116 assigned negative charge : -360.8336 centred at (gu) : 86.87051 91.94837 93.81302 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20798 grid for indexing accessible points = 1.400000 m= 28313 mr = 53083 m= 4752 mr = 20849 m= 436 mr = 2942 m= 6 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.3800000 number of dielectric boundary points 33357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17822 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) : 0.6753296 object centre at (A) : 19.68700 12.40650 22.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2918874E-02 1.1200258E-02 midg,1,midg; midg,igrid,midg 1.7559478E-02 -2.1143584E-02 1,midg,midg; igrid,midg,midg 4.9396601E-02 -2.6529552E-03 gauss-seidel spectral radius is 0.9987680 estimated iterations to convergence 226 setup time was (sec) 0.6000000 now iterating at: 12:55:32 rms-change max change #iterations 4.589356 187.8010 at 10iterations 2.228998 83.88356 at 20iterations 1.084902 39.57669 at 30iterations 0.5266795 16.05257 at 40iterations 0.2567005 8.720615 at 50iterations 0.1245588 3.924427 at 60iterations 6.0889222E-02 1.808593 at 70iterations 2.9843183E-02 0.9317474 at 80iterations 1.4642945E-02 0.4388853 at 90iterations 7.2668791E-03 0.2083101 at 100iterations 3.6766585E-03 0.1315956 at 110iterations 1.9306848E-03 5.9665680E-02 at 120iterations finished qdiffx linear iterations at : 12:55:39 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 1.9306848E-03 5.9665680E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 12:55:40 8.140u 0.247s 0:08.71 96.2% 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 Sat Oct 15 2011 at 12:55:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.038983 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): -4.843000 44.21700 ymin,ymax (A): -13.95100 38.76400 zmin,zma (A): -0.5230000 44.57600 x,y,z range (A): 49.06000 52.71500 45.09900 scale (grids/A): 3.038983 object centre (A): 19.68700 12.40650 22.02650 number of atom coordinates read : 2393 total number of charged atoms : 2252 net assigned charge : 4.500014 assigned positive charge : 365.3330 centred at (gu) : 85.12937 92.41356 95.38661 assigned negative charge : -360.8336 centred at (gu) : 85.30563 92.92255 95.71939 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 177682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20798 grid for indexing accessible points = 1.400000 m= 90709 mr = 128237 m= 33652 mr = 74088 m= 8756 mr = 27161 m= 1747 mr = 6453 m= 183 mr = 1304 m= 4 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 494 time to turn everything in is 1.000000 number of dielectric boundary points 75388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 18010 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) : 2.025989 object centre at (A) : 19.68700 12.40650 22.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2771724 -2.9148092E-02 midg,1,midg; midg,igrid,midg 0.4181860 -0.1732687 1,midg,midg; igrid,midg,midg 0.6843283 -0.1973848 gauss-seidel spectral radius is 0.9992824 estimated iterations to convergence 295 setup time was (sec) 1.260000 now iterating at: 12:55:41 rms-change max change #iterations 10.48946 409.6559 at 10iterations 6.153781 136.5429 at 20iterations 3.621913 73.76983 at 30iterations 2.113559 42.01536 at 40iterations 1.236198 22.86697 at 50iterations 0.7214342 13.04985 at 60iterations 0.4208329 7.803793 at 70iterations 0.2453575 4.188190 at 80iterations 0.1428021 2.515896 at 90iterations 8.3343521E-02 1.575759 at 100iterations 4.8564758E-02 0.8462505 at 110iterations 2.8532594E-02 0.5073776 at 120iterations 1.6922444E-02 0.3180618 at 130iterations 1.0213223E-02 0.2319908 at 140iterations 6.3599539E-03 0.1333389 at 150iterations 4.1526272E-03 9.1171265E-02 at 160iterations 2.8874865E-03 6.1592102E-02 at 170iterations 2.1315201E-03 4.4944763E-02 at 180iterations finished qdiffx linear iterations at : 12:55:53 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 2.1315201E-03 4.4944763E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 12:55:54 13.360u 0.244s 0:13.95 97.4% 0+0k 0+0io 0pf+0w