Sat Oct 8 20:23:54 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 20:23:54 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 = 2563 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: 0.7079364 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 0.7079364 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 4.000004 assigned positive charge : 384.0931 centred at (gu) : 88.54646 87.96684 89.46630 assigned negative charge : -380.0937 centred at (gu) : 88.42833 87.86382 89.54848 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8637 nv = 96 ne = 84 npr = 54225 no. pairs analyzed = 54225 no. exposed pairs = 2938 no. arc points = 21309 no. surface atoms = 987 nbur = 1576 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 561 mr = 5074 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 347 time to turn everything in is 0.3000000 number of dielectric boundary points 4026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1932 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9803 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5005909E-08 -1.2191557E-08 midg,1,midg; midg,igrid,midg -4.1411887E-08 6.6172134E-08 1,midg,midg; igrid,midg,midg -4.8981175E-08 8.0634287E-08 gauss-seidel spectral radius is 0.9896461 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 20:23:55 rms-change max change #iterations 0.2293580 33.53173 at 10iterations 2.8555235E-02 3.630447 at 20iterations 3.5463625E-03 0.4046817 at 30iterations 4.3404623E-04 6.3053131E-02 at 40iterations 5.4433112E-05 7.9574585E-03 at 50iterations finished qdiffx linear iterations at : 20:23:57 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 5.4433112E-05 7.9574585E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 20:23:58 3.209u 0.157s 0:03.64 92.0% 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 20:23:58 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 = 2563 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: 2.123809 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 2.123809 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 4.000004 assigned positive charge : 384.0931 centred at (gu) : 85.63875 83.90018 88.39837 assigned negative charge : -380.0937 centred at (gu) : 85.28484 83.59119 88.64525 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 36298 mr = 66068 m= 6819 mr = 28002 m= 665 mr = 4726 m= 7 mr = 357 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 9527 time to turn everything in is 0.6300000 number of dielectric boundary points 37079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19247 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) : 0.7079364 object centre at (A) : -2.332500 14.14350 -15.93400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7744628E-02 4.8844730E-03 midg,1,midg; midg,igrid,midg -3.8270943E-02 1.0321178E-03 1,midg,midg; igrid,midg,midg -1.7199889E-02 0.1186658 gauss-seidel spectral radius is 0.9988753 estimated iterations to convergence 236 setup time was (sec) 0.9200000 now iterating at: 20:23:59 rms-change max change #iterations 5.166923 200.7355 at 10iterations 2.573658 90.68593 at 20iterations 1.292463 37.19230 at 30iterations 0.6506182 18.68888 at 40iterations 0.3271794 8.556735 at 50iterations 0.1640793 4.319086 at 60iterations 8.2590915E-02 2.230281 at 70iterations 4.1504052E-02 1.196331 at 80iterations 2.0797797E-02 0.5892415 at 90iterations 1.0431807E-02 0.2818832 at 100iterations 5.2689398E-03 0.1468978 at 110iterations 2.6448874E-03 7.1218491E-02 at 120iterations finished qdiffx linear iterations at : 20:24:05 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 2.6448874E-03 7.1218491E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 20:24:05 7.102u 0.154s 0:07.52 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 Sat Oct 8 2011 at 20:24:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 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: 3.185714 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 3.185714 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 4.000004 assigned positive charge : 384.0931 centred at (gu) : 83.45814 80.85010 87.59735 assigned negative charge : -380.0937 centred at (gu) : 82.92713 80.38681 87.96781 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 213022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 114029 mr = 158425 m= 45936 mr = 96097 m= 12996 mr = 38334 m= 2633 mr = 10331 m= 315 mr = 2007 m= 7 mr = 213 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 32087 time to turn everything in is 2.110000 number of dielectric boundary points 83529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 19384 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) : 2.123809 object centre at (A) : -2.332500 14.14350 -15.93400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2050115 0.1373220 midg,1,midg; midg,igrid,midg -0.1481934 -0.1227819 1,midg,midg; igrid,midg,midg -0.2367048 1.608584 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.430000 now iterating at: 20:24:08 rms-change max change #iterations 11.27478 396.3932 at 10iterations 6.613786 121.5519 at 20iterations 3.881882 78.43119 at 30iterations 2.278653 38.88383 at 40iterations 1.334944 21.15662 at 50iterations 0.7816830 13.09778 at 60iterations 0.4597183 7.116373 at 70iterations 0.2697996 4.104382 at 80iterations 0.1578929 2.562504 at 90iterations 9.2611074E-02 1.350677 at 100iterations 5.4358907E-02 0.8746166 at 110iterations 3.1859644E-02 0.5264168 at 120iterations 1.8664356E-02 0.3143806 at 130iterations 1.0944271E-02 0.1765550 at 140iterations 6.4166347E-03 0.1044579 at 150iterations 3.7615681E-03 5.9768677E-02 at 160iterations 2.2067886E-03 3.5518646E-02 at 170iterations 1.2949831E-03 2.1454811E-02 at 180iterations finished qdiffx linear iterations at : 20:24:17 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 1.2949831E-03 2.1454811E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 20:24:18 12.245u 0.175s 0:12.73 97.4% 0+0k 0+0io 0pf+0w