Sat Oct 8 18:23:47 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 18:23:47 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3793 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5304329 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 0.5304329 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999967 assigned positive charge : 577.7333 centred at (gu) : 88.80528 85.86188 90.55740 assigned negative charge : -584.7358 centred at (gu) : 88.85857 85.81952 90.54910 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6920 nv = 96 ne = 84 npr = 76208 no. pairs analyzed = 76208 no. exposed pairs = 4961 no. arc points = 34591 no. surface atoms = 1645 nbur = 2148 mkacc time = 0.2100000 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 = 1.596000 m= 277 mr = 3504 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3495 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2689475E-10 -2.0951402E-10 midg,1,midg; midg,igrid,midg -1.2269642E-09 -1.2415881E-11 1,midg,midg; igrid,midg,midg 3.9805645E-11 -3.5020203E-10 gauss-seidel spectral radius is 0.9817500 estimated iterations to convergence 61 setup time was (sec) 0.7100000 now iterating at: 18:23:48 rms-change max change #iterations 7.0815586E-02 13.95283 at 10iterations 4.4544688E-03 0.7252026 at 20iterations 3.2817779E-04 5.0521851E-02 at 30iterations 4.9676106E-05 9.8323822E-03 at 40iterations 1.2203505E-05 2.4394989E-03 at 50iterations finished qdiffx linear iterations at : 18:23:51 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 1.2203505E-05 2.4394989E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 18:23:52 4.633u 0.414s 0:05.31 94.9% 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 18:23:52 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3793 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: 1.591299 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 1.591299 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999967 assigned positive charge : 577.7333 centred at (gu) : 86.41460 77.58459 91.67105 assigned negative charge : -584.7358 centred at (gu) : 86.57552 77.45809 91.64693 start vw surface at 0.7900000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 77256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23115 mr = 52126 m= 2195 mr = 15214 m= 59 mr = 907 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 34378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 27656 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) : 0.5304329 object centre at (A) : 29.24450 15.13850 26.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0761533E-04 -4.7902657E-05 midg,1,midg; midg,igrid,midg -2.7440293E-02 8.4639067E-04 1,midg,midg; igrid,midg,midg -8.1630070E-03 -2.1750258E-02 gauss-seidel spectral radius is 0.9981561 estimated iterations to convergence 185 setup time was (sec) 2.040000 now iterating at: 18:23:54 rms-change max change #iterations 3.650491 159.7310 at 10iterations 1.503310 53.40659 at 20iterations 0.6221347 19.71701 at 30iterations 0.2581581 8.534090 at 40iterations 0.1069629 3.977909 at 50iterations 4.4405516E-02 1.548191 at 60iterations 1.8409599E-02 0.6049919 at 70iterations 7.6178685E-03 0.2757552 at 80iterations 3.1763152E-03 0.1167021 at 90iterations 1.3270814E-03 4.7546864E-02 at 100iterations 5.6119682E-04 1.9744873E-02 at 110iterations 2.4252037E-04 9.1452301E-03 at 120iterations finished qdiffx linear iterations at : 18:24:04 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 2.4252037E-04 9.1452301E-03 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 18:24:05 11.934u 0.480s 0:12.73 97.4% 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 Sat Oct 8 2011 at 18:24:05 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3793 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.386948 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 2.386948 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999967 assigned positive charge : 577.7333 centred at (gu) : 84.62150 71.37658 92.50637 assigned negative charge : -584.7358 centred at (gu) : 84.86320 71.18716 92.47025 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 81264 mr = 128180 m= 21434 mr = 62964 m= 3154 mr = 15273 m= 164 mr = 1800 m= 4 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 77533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 29101 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) : 1.591299 object centre at (A) : 29.24450 15.13850 26.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3003977E-03 0.2040120 midg,1,midg; midg,igrid,midg -0.4607018 1.5959568E-02 1,midg,midg; igrid,midg,midg -0.1206926 -0.4298449 gauss-seidel spectral radius is 0.9991440 estimated iterations to convergence 270 setup time was (sec) 1.910000 now iterating at: 18:24:07 rms-change max change #iterations 9.605116 341.3629 at 10iterations 5.420446 158.9098 at 20iterations 3.035953 70.28186 at 30iterations 1.697147 37.40823 at 40iterations 0.9434840 18.98331 at 50iterations 0.5241550 11.01192 at 60iterations 0.2904659 7.069889 at 70iterations 0.1609498 3.412483 at 80iterations 8.8996470E-02 1.714359 at 90iterations 4.9160849E-02 1.018598 at 100iterations 2.7089013E-02 0.5450401 at 110iterations 1.4957354E-02 0.2850494 at 120iterations 8.2611945E-03 0.1684179 at 130iterations 4.5623318E-03 8.2485199E-02 at 140iterations 2.5213128E-03 5.1868439E-02 at 150iterations 1.3965494E-03 2.8169155E-02 at 160iterations 7.7946187E-04 1.6175270E-02 at 170iterations 4.3814391E-04 8.4881783E-03 at 180iterations finished qdiffx linear iterations at : 18:24:23 total time elapsed so far: 18.30000 # loops : 180 mean,max change (kT/e) : 4.3814391E-04 8.4881783E-03 energy calculations done at 18.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.46000 DelPhi exited at 18:24:24 18.461u 0.497s 0:19.22 98.5% 0+0k 0+0io 0pf+0w