Sun Oct 9 08:16:42 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 Sun Oct 9 2011 at 08:16:42 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5273 !!! WARNING: HIR 704 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5502914 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 0.5502914 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.485982 assigned positive charge : 793.6085 centred at (gu) : 90.75327 91.12032 89.09880 assigned negative charge : -797.1008 centred at (gu) : 90.73217 91.10646 88.96966 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10344 nv = 96 ne = 84 npr = 105295 no. pairs analyzed = 105295 no. exposed pairs = 6988 no. arc points = 48275 no. surface atoms = 2332 nbur = 2941 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 416 mr = 5264 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 5479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4745 ## 562 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5955329E-09 1.2209279E-09 midg,1,midg; midg,igrid,midg -3.3214884E-10 -6.0159787E-11 1,midg,midg; igrid,midg,midg -4.4673595E-10 6.5103117E-11 gauss-seidel spectral radius is 0.9831516 estimated iterations to convergence 63 setup time was (sec) 0.7000000 now iterating at: 08:16:43 rms-change max change #iterations 0.1037204 12.50691 at 10iterations 7.3680500E-03 0.9474754 at 20iterations 7.2196475E-04 0.1298332 at 30iterations 1.5007185E-04 2.8886795E-02 at 40iterations 4.4464894E-05 8.3599091E-03 at 50iterations finished qdiffx linear iterations at : 08:16:46 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.4464894E-05 8.3599091E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:16:46 3.467u 0.187s 0:04.08 89.2% 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 Sun Oct 9 2011 at 08:16:46 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5273 !!! WARNING: HIR 704 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.650874 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 1.650874 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.485982 assigned positive charge : 793.6085 centred at (gu) : 92.25864 93.35963 87.29470 assigned negative charge : -797.1008 centred at (gu) : 92.19614 93.31927 86.90880 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 113645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 35765 mr = 76645 m= 4045 mr = 24312 m= 117 mr = 2020 m= 0 mr = 13 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.7700000 number of dielectric boundary points 50582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 484 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 39175 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) : 0.5502914 object centre at (A) : 14.71250 36.91100 -78.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9572531E-02 2.4110977E-02 midg,1,midg; midg,igrid,midg -8.4976861E-03 -7.7139456E-03 1,midg,midg; igrid,midg,midg -4.3648649E-03 -1.4835864E-02 gauss-seidel spectral radius is 0.9984588 estimated iterations to convergence 202 setup time was (sec) 1.060000 now iterating at: 08:16:48 rms-change max change #iterations 4.799331 164.0274 at 10iterations 2.125988 65.65184 at 20iterations 0.9494878 26.06325 at 30iterations 0.4253828 12.21930 at 40iterations 0.1896460 5.838531 at 50iterations 8.4880516E-02 2.721703 at 60iterations 3.7915330E-02 1.188803 at 70iterations 1.6986722E-02 0.5331879 at 80iterations 7.6147094E-03 0.2090569 at 90iterations 3.4154817E-03 9.2346191E-02 at 100iterations 1.5396714E-03 4.5343876E-02 at 110iterations 6.9871859E-04 1.9870758E-02 at 120iterations finished qdiffx linear iterations at : 08:16:54 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 6.9871859E-04 1.9870758E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:16:55 7.927u 0.229s 0:08.44 96.4% 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 Sun Oct 9 2011 at 08:16:55 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5273 !!! WARNING: HIR 704 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.476311 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 2.476311 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.485982 assigned positive charge : 793.6085 centred at (gu) : 93.38752 95.03881 85.94157 assigned negative charge : -797.1008 centred at (gu) : 93.29409 94.97886 85.36302 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 263973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48275 grid for indexing accessible points = 1.400000 m= 122923 mr = 188201 m= 36024 mr = 96028 m= 6490 mr = 26831 m= 541 mr = 4358 m= 11 mr = 270 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 1.890000 number of dielectric boundary points 114274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 40820 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) : 1.650874 object centre at (A) : 14.71250 36.91100 -78.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9656931 0.2575195 midg,1,midg; midg,igrid,midg -8.2068238E-03 2.1803040E-02 1,midg,midg; igrid,midg,midg -0.2825850 5.9320242E-04 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 2.230000 now iterating at: 08:16:57 rms-change max change #iterations 12.36755 410.2507 at 10iterations 7.446934 175.8469 at 20iterations 4.470434 108.8590 at 30iterations 2.667164 59.10201 at 40iterations 1.576678 29.52231 at 50iterations 0.9332213 16.23369 at 60iterations 0.5507116 9.166397 at 70iterations 0.3238923 6.134430 at 80iterations 0.1898264 3.084198 at 90iterations 0.1112089 1.985575 at 100iterations 6.5147690E-02 1.117320 at 110iterations 3.8151637E-02 0.5943699 at 120iterations 2.2298040E-02 0.4062507 at 130iterations 1.3026227E-02 0.2267609 at 140iterations 7.6126638E-03 0.1205444 at 150iterations 4.4607953E-03 7.4307680E-02 at 160iterations 2.6053684E-03 4.1686058E-02 at 170iterations 1.5301136E-03 2.3731232E-02 at 180iterations finished qdiffx linear iterations at : 08:17:10 total time elapsed so far: 14.60000 # loops : 180 mean,max change (kT/e) : 1.5301136E-03 2.3731232E-02 energy calculations done at 14.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.79000 DelPhi exited at 08:17:10 14.789u 0.249s 0:15.44 97.2% 0+0k 0+0io 0pf+0w