Sat Oct 8 17:07:23 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 8 2011 at 17:07:23 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 = 3553 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5160243 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 0.5160243 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -6.999988 assigned positive charge : 536.1942 centred at (gu) : 90.13036 87.72855 89.32821 assigned negative charge : -543.1957 centred at (gu) : 90.13522 87.79024 89.35406 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5903 nv = 96 ne = 84 npr = 72628 no. pairs analyzed = 72628 no. exposed pairs = 4372 no. arc points = 30556 no. surface atoms = 1469 nbur = 2084 mkacc time = 0.1900000 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 = 1.652000 m= 216 mr = 3112 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3006 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8015 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7924660E-11 -1.6296799E-10 midg,1,midg; midg,igrid,midg 4.5189092E-11 -1.5806566E-10 1,midg,midg; igrid,midg,midg -1.1389427E-10 -1.4641632E-10 gauss-seidel spectral radius is 0.9806980 estimated iterations to convergence 59 setup time was (sec) 0.7100000 now iterating at: 17:07:24 rms-change max change #iterations 5.9381727E-02 9.846664 at 10iterations 3.4317030E-03 0.5496750 at 20iterations 2.3786401E-04 4.1064262E-02 at 30iterations 3.5274945E-05 7.3032379E-03 at 40iterations 8.2424331E-06 1.7356873E-03 at 50iterations finished qdiffx linear iterations at : 17:07:28 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 8.2424331E-06 1.7356873E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:07:29 4.701u 0.390s 0:05.35 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 17:07:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3553 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.548073 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 1.548073 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -6.999988 assigned positive charge : 536.1942 centred at (gu) : 90.38980 83.18474 87.98367 assigned negative charge : -543.1957 centred at (gu) : 90.40527 83.37048 88.06191 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19740 mr = 45798 m= 1811 mr = 13374 m= 35 mr = 843 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.5600000 number of dielectric boundary points 28216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25766 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) : 0.5160243 object centre at (A) : 29.53950 45.16700 10.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8197342E-04 -1.4247153E-03 midg,1,midg; midg,igrid,midg -1.4472960E-02 -1.4730187E-02 1,midg,midg; igrid,midg,midg 1.0451771E-02 -2.7881679E-03 gauss-seidel spectral radius is 0.9980161 estimated iterations to convergence 178 setup time was (sec) 0.8700000 now iterating at: 17:07:30 rms-change max change #iterations 3.242749 169.4324 at 10iterations 1.295791 56.11809 at 20iterations 0.5216214 18.49861 at 30iterations 0.2092430 8.019676 at 40iterations 8.4102891E-02 3.175560 at 50iterations 3.3648562E-02 1.185123 at 60iterations 1.3576812E-02 0.5615501 at 70iterations 5.4561747E-03 0.1954365 at 80iterations 2.1972354E-03 8.5201263E-02 at 90iterations 8.8825379E-04 3.1538010E-02 at 100iterations 3.6249682E-04 1.2184143E-02 at 110iterations 1.5026091E-04 5.3141117E-03 at 120iterations finished qdiffx linear iterations at : 17:07:40 total time elapsed so far: 11.23000 # loops : 120 mean,max change (kT/e) : 1.5026091E-04 5.3141117E-03 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 17:07:41 11.395u 0.446s 0:12.13 97.5% 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 17:07:41 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 = 3553 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.322109 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 2.322109 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -6.999988 assigned positive charge : 536.1942 centred at (gu) : 90.58466 79.77676 86.97524 assigned negative charge : -543.1957 centred at (gu) : 90.60779 80.05569 87.09268 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 155502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70236 mr = 112606 m= 18133 mr = 55313 m= 2673 mr = 13226 m= 144 mr = 1692 m= 0 mr = 40 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 1.370000 number of dielectric boundary points 63811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 27178 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) : 1.548073 object centre at (A) : 29.53950 45.16700 10.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8547107E-03 -1.5057021E-02 midg,1,midg; midg,igrid,midg -0.3059361 -0.2909958 1,midg,midg; igrid,midg,midg 0.4266860 -4.9356472E-02 gauss-seidel spectral radius is 0.9990893 estimated iterations to convergence 262 setup time was (sec) 1.760000 now iterating at: 17:07:43 rms-change max change #iterations 8.710782 290.1060 at 10iterations 4.837687 121.0334 at 20iterations 2.667923 68.93362 at 30iterations 1.462859 33.80705 at 40iterations 0.8005675 18.80888 at 50iterations 0.4348984 9.044451 at 60iterations 0.2363476 5.594615 at 70iterations 0.1286420 3.120984 at 80iterations 6.9807492E-02 1.479020 at 90iterations 3.7850682E-02 0.7502117 at 100iterations 2.0478358E-02 0.4594116 at 110iterations 1.1108734E-02 0.2417798 at 120iterations 6.0024690E-03 0.1241341 at 130iterations 3.2494252E-03 7.0664644E-02 at 140iterations 1.7586121E-03 3.6676407E-02 at 150iterations 9.5472945E-04 1.9501686E-02 at 160iterations 5.1720871E-04 1.0748386E-02 at 170iterations 2.8190436E-04 5.8236122E-03 at 180iterations finished qdiffx linear iterations at : 17:08:03 total time elapsed so far: 22.10000 # loops : 180 mean,max change (kT/e) : 2.8190436E-04 5.8236122E-03 energy calculations done at 22.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.27000 DelPhi exited at 17:08:04 22.274u 0.472s 0:23.04 98.6% 0+0k 0+0io 0pf+0w