Sat Oct 8 13:39:02 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 8 2011 at 13:39:02 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIR 110 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6386223 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 0.6386223 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.014008 assigned positive charge : 444.1586 centred at (gu) : 88.61584 89.97856 91.81242 assigned negative charge : -442.1454 centred at (gu) : 88.55442 89.89749 91.70786 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8080 nv = 96 ne = 84 npr = 61797 no. pairs analyzed = 61797 no. exposed pairs = 3437 no. arc points = 23968 no. surface atoms = 1172 nbur = 1811 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4686 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9812 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2517863E-09 2.3541896E-08 midg,1,midg; midg,igrid,midg -7.7793763E-09 1.2839173E-08 1,midg,midg; igrid,midg,midg -7.1239845E-09 7.7649336E-09 gauss-seidel spectral radius is 0.9873254 estimated iterations to convergence 73 setup time was (sec) 0.7500000 now iterating at: 13:39:03 rms-change max change #iterations 0.1551046 22.93630 at 10iterations 1.5862083E-02 2.203104 at 20iterations 1.6831489E-03 0.2175026 at 30iterations 2.0652628E-04 3.1757355E-02 at 40iterations 3.1677831E-05 4.6691895E-03 at 50iterations finished qdiffx linear iterations at : 13:39:07 total time elapsed so far: 5.250000 # loops : 50 mean,max change (kT/e) : 3.1677831E-05 4.6691895E-03 energy calculations done at 5.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.420000 DelPhi exited at 13:39:08 5.428u 0.443s 0:06.16 95.1% 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 8 2011 at 13:39:08 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIR 110 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.915867 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 1.915867 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.014008 assigned positive charge : 444.1586 centred at (gu) : 85.84708 89.93500 95.43644 assigned negative charge : -442.1454 centred at (gu) : 85.66310 89.69220 95.12327 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23968 grid for indexing accessible points = 1.400000 m= 32160 mr = 63203 m= 4955 mr = 24208 m= 302 mr = 3034 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 34791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22319 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) : 0.6386223 object centre at (A) : 15.76950 -0.3254995 19.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5636601E-02 2.0398485E-02 midg,1,midg; midg,igrid,midg 2.8467826E-03 2.0299694E-02 1,midg,midg; igrid,midg,midg -3.6198065E-02 1.5750546E-02 gauss-seidel spectral radius is 0.9986817 estimated iterations to convergence 218 setup time was (sec) 1.080000 now iterating at: 13:39:09 rms-change max change #iterations 4.628389 188.4830 at 10iterations 2.193538 69.00471 at 20iterations 1.043163 33.80859 at 30iterations 0.4968263 14.56599 at 40iterations 0.2358737 6.885532 at 50iterations 0.1122050 3.082543 at 60iterations 5.3344365E-02 1.713068 at 70iterations 2.5313700E-02 0.7509727 at 80iterations 1.2050119E-02 0.3278732 at 90iterations 5.7339449E-03 0.1722260 at 100iterations 2.7209325E-03 7.7087402E-02 at 110iterations 1.2997496E-03 3.6872387E-02 at 120iterations finished qdiffx linear iterations at : 13:39:22 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 1.2997496E-03 3.6872387E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 13:39:22 13.396u 0.519s 0:14.18 98.0% 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 8 2011 at 13:39:22 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIR 110 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.873800 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 2.873800 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.014008 assigned positive charge : 444.1586 centred at (gu) : 83.77045 89.90256 98.15464 assigned negative charge : -442.1454 centred at (gu) : 83.49451 89.53828 97.68487 start vw surface at 0.1200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 203854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23968 grid for indexing accessible points = 1.400000 m= 104612 mr = 152916 m= 37223 mr = 87038 m= 8889 mr = 30084 m= 1335 mr = 6621 m= 94 mr = 889 m= 0 mr = 43 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 78416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 22686 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) : 1.915867 object centre at (A) : 15.76950 -0.3254995 19.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3661329E-02 0.2653419 midg,1,midg; midg,igrid,midg 2.7140902E-02 0.2479339 1,midg,midg; igrid,midg,midg -0.4918925 0.1984601 gauss-seidel spectral radius is 0.9992768 estimated iterations to convergence 293 setup time was (sec) 2.330000 now iterating at: 13:39:25 rms-change max change #iterations 10.82743 461.5608 at 10iterations 6.373312 119.3149 at 20iterations 3.737531 78.58362 at 30iterations 2.183379 42.87347 at 40iterations 1.272144 23.72059 at 50iterations 0.7416087 12.57854 at 60iterations 0.4310069 7.882842 at 70iterations 0.2501937 4.297447 at 80iterations 0.1452069 2.663529 at 90iterations 8.4247760E-02 1.384208 at 100iterations 4.8654046E-02 0.7947855 at 110iterations 2.8266897E-02 0.4817581 at 120iterations 1.6389791E-02 0.2693195 at 130iterations 9.5086936E-03 0.1667824 at 140iterations 5.5243834E-03 8.8516235E-02 at 150iterations 3.2064626E-03 5.5191040E-02 at 160iterations 1.8675327E-03 3.3182144E-02 at 170iterations 1.0964831E-03 1.7372131E-02 at 180iterations finished qdiffx linear iterations at : 13:39:45 total time elapsed so far: 22.90000 # loops : 180 mean,max change (kT/e) : 1.0964831E-03 1.7372131E-02 energy calculations done at 22.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.07000 DelPhi exited at 13:39:46 23.078u 0.540s 0:23.89 98.8% 0+0k 0+0io 0pf+0w