Tue Oct 11 03:51:43 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 03:51:43 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6614764 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 0.6614764 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2608 net assigned charge : 1.162015 assigned positive charge : 415.1437 centred at (gu) : 90.08170 90.43797 91.22533 assigned negative charge : -413.9823 centred at (gu) : 89.77643 90.30532 91.18370 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8079 nv = 96 ne = 84 npr = 57076 no. pairs analyzed = 57076 no. exposed pairs = 3211 no. arc points = 22532 no. surface atoms = 1087 nbur = 1674 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4735 m= 5 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2000000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2231 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9557 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8153632E-09 1.5466991E-08 midg,1,midg; midg,igrid,midg -2.4208816E-08 3.4568156E-08 1,midg,midg; igrid,midg,midg -6.5024565E-08 6.8768585E-08 gauss-seidel spectral radius is 0.9881632 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 03:51:44 rms-change max change #iterations 0.1740834 22.49248 at 10iterations 1.8597031E-02 2.550192 at 20iterations 2.0152300E-03 0.2414846 at 30iterations 2.1861830E-04 2.8870106E-02 at 40iterations 2.4396832E-05 3.0632019E-03 at 50iterations finished qdiffx linear iterations at : 03:51:47 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.4396832E-05 3.0632019E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:51:47 3.321u 0.181s 0:03.90 89.7% 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 03:51:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.984429 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 1.984429 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2608 net assigned charge : 1.162015 assigned positive charge : 415.1437 centred at (gu) : 90.24452 91.31339 93.67564 assigned negative charge : -413.9823 centred at (gu) : 89.32915 90.91572 93.55078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22532 grid for indexing accessible points = 1.400000 m= 33548 mr = 62157 m= 5453 mr = 25552 m= 330 mr = 3445 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 439 time to turn everything in is 0.4200000 number of dielectric boundary points 34592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20553 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) : 0.6614764 object centre at (A) : 12.88600 -2.603000 18.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2701338E-02 -4.0251720E-03 midg,1,midg; midg,igrid,midg -1.7431244E-02 2.3776578E-02 1,midg,midg; igrid,midg,midg -2.0423144E-02 8.0058731E-02 gauss-seidel spectral radius is 0.9987497 estimated iterations to convergence 224 setup time was (sec) 0.6300000 now iterating at: 03:51:48 rms-change max change #iterations 4.769341 223.1909 at 10iterations 2.317165 79.90406 at 20iterations 1.124229 33.79398 at 30iterations 0.5449280 16.01780 at 40iterations 0.2650429 7.696130 at 50iterations 0.1282285 3.570188 at 60iterations 6.2236976E-02 1.952881 at 70iterations 3.0162480E-02 0.9398727 at 80iterations 1.4688431E-02 0.4074020 at 90iterations 7.1105687E-03 0.2284536 at 100iterations 3.4535883E-03 9.9826336E-02 at 110iterations 1.6763968E-03 4.8416048E-02 at 120iterations finished qdiffx linear iterations at : 03:51:55 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.6763968E-03 4.8416048E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 03:51:55 7.713u 0.203s 0:08.25 95.8% 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 Tue Oct 11 2011 at 03:51:55 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.976644 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): -11.34700 37.11900 ymin,ymax (A): -26.84400 21.63800 zmin,zma (A): -8.224999 45.59400 x,y,z range (A): 48.46600 48.48200 53.81900 scale (grids/A): 2.976644 object centre (A): 12.88600 -2.603000 18.68450 number of atom coordinates read : 2761 total number of charged atoms : 2608 net assigned charge : 1.162015 assigned positive charge : 415.1437 centred at (gu) : 90.36662 91.96989 95.51328 assigned negative charge : -413.9823 centred at (gu) : 88.99367 91.37341 95.32612 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 199994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22532 grid for indexing accessible points = 1.400000 m= 106474 mr = 149645 m= 40623 mr = 89160 m= 9886 mr = 33296 m= 1465 mr = 7419 m= 106 mr = 927 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1327 time to turn everything in is 1.110000 number of dielectric boundary points 78063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 20848 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) : 1.984429 object centre at (A) : 12.88600 -2.603000 18.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2392381 0.2199930 midg,1,midg; midg,igrid,midg -0.1939039 0.3346438 1,midg,midg; igrid,midg,midg -7.4881449E-02 0.6816993 gauss-seidel spectral radius is 0.9992843 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 03:51:57 rms-change max change #iterations 10.89387 408.5093 at 10iterations 6.410903 135.9810 at 20iterations 3.760989 69.84871 at 30iterations 2.202351 40.10326 at 40iterations 1.288266 23.01477 at 50iterations 0.7504989 12.38318 at 60iterations 0.4389098 7.115999 at 70iterations 0.2557259 4.426151 at 80iterations 0.1490139 2.710648 at 90iterations 8.6542860E-02 1.588352 at 100iterations 5.0403707E-02 0.8545750 at 110iterations 2.9324204E-02 0.4778774 at 120iterations 1.7079554E-02 0.2800846 at 130iterations 9.9320784E-03 0.1806581 at 140iterations 5.7942867E-03 9.9306107E-02 at 150iterations 3.3899697E-03 5.4599762E-02 at 160iterations 1.9843224E-03 3.9501667E-02 at 170iterations 1.1721206E-03 2.1411896E-02 at 180iterations finished qdiffx linear iterations at : 03:52:08 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 1.1721206E-03 2.1411896E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 03:52:09 12.781u 0.217s 0:13.31 97.5% 0+0k 0+0io 0pf+0w