Sat Oct 8 17:55:32 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 17:55:32 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3535 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: 0.5495269 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 0.5495269 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499991 assigned positive charge : 537.1638 centred at (gu) : 88.38980 88.86805 91.39090 assigned negative charge : -541.6658 centred at (gu) : 88.37595 88.84273 91.42535 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6909 nv = 96 ne = 84 npr = 71766 no. pairs analyzed = 71766 no. exposed pairs = 4468 no. arc points = 30248 no. surface atoms = 1504 nbur = 2031 mkacc time = 0.1800000 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= 286 mr = 3677 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0959709E-13 -8.8273899E-10 midg,1,midg; midg,igrid,midg -7.1555545E-10 -6.1896759E-11 1,midg,midg; igrid,midg,midg -6.4672173E-10 -1.2641645E-10 gauss-seidel spectral radius is 0.9829645 estimated iterations to convergence 63 setup time was (sec) 0.7000000 now iterating at: 17:55:33 rms-change max change #iterations 8.6859055E-02 15.87463 at 10iterations 6.0331784E-03 0.9627724 at 20iterations 5.3240953E-04 8.1746101E-02 at 30iterations 1.1358681E-04 2.1699905E-02 at 40iterations 3.5205041E-05 7.0333481E-03 at 50iterations finished qdiffx linear iterations at : 17:55:36 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 3.5205041E-05 7.0333481E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 17:55:37 4.282u 0.222s 0:04.76 94.5% 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 17:55:37 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3535 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: 1.648581 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 1.648581 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499991 assigned positive charge : 537.1638 centred at (gu) : 85.16859 86.60281 94.17163 assigned negative charge : -541.6658 centred at (gu) : 85.12767 86.52792 94.27571 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25042 mr = 53599 m= 2712 mr = 17454 m= 69 mr = 1349 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.6500000 number of dielectric boundary points 32478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25944 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) : 0.5495269 object centre at (A) : 29.16650 1.240500 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8165315E-03 -1.9359726E-03 midg,1,midg; midg,igrid,midg -7.6642255E-03 -8.7913394E-04 1,midg,midg; igrid,midg,midg -6.2607876E-03 7.6681389E-03 gauss-seidel spectral radius is 0.9982676 estimated iterations to convergence 191 setup time was (sec) 0.9700000 now iterating at: 17:55:38 rms-change max change #iterations 3.823812 198.9088 at 10iterations 1.624502 57.57721 at 20iterations 0.6932920 21.89870 at 30iterations 0.2935504 9.725435 at 40iterations 0.1252421 4.416222 at 50iterations 5.3462617E-02 2.051563 at 60iterations 2.2788331E-02 0.7523422 at 70iterations 9.7771473E-03 0.3377457 at 80iterations 4.2223646E-03 0.1630116 at 90iterations 1.8615638E-03 6.6947937E-02 at 100iterations 8.5141003E-04 3.2110453E-02 at 110iterations 4.2376562E-04 1.6730547E-02 at 120iterations finished qdiffx linear iterations at : 17:55:46 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 4.2376562E-04 1.6730547E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 17:55:47 9.552u 0.278s 0:10.13 96.9% 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 17:55:47 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3535 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: 2.472871 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 2.472871 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499991 assigned positive charge : 537.1638 centred at (gu) : 82.75260 84.90409 96.25717 assigned negative charge : -541.6658 centred at (gu) : 82.69138 84.79195 96.41348 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 178787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30248 grid for indexing accessible points = 1.400000 m= 85827 mr = 130570 m= 25576 mr = 68717 m= 4337 mr = 19329 m= 311 mr = 2809 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 202 time to turn everything in is 1.530000 number of dielectric boundary points 73319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 27077 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) : 1.648581 object centre at (A) : 29.16650 1.240500 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7575997E-02 4.5208335E-02 midg,1,midg; midg,igrid,midg -0.1024244 5.2972598E-04 1,midg,midg; igrid,midg,midg -7.9218097E-02 0.1679064 gauss-seidel spectral radius is 0.9991701 estimated iterations to convergence 274 setup time was (sec) 1.910000 now iterating at: 17:55:49 rms-change max change #iterations 9.751196 324.6489 at 10iterations 5.540702 129.6754 at 20iterations 3.138983 64.40248 at 30iterations 1.766870 40.28666 at 40iterations 0.9930660 20.11796 at 50iterations 0.5553035 10.70898 at 60iterations 0.3107261 6.386962 at 70iterations 0.1735830 3.425244 at 80iterations 9.6728362E-02 1.789703 at 90iterations 5.4152641E-02 1.054129 at 100iterations 3.0145884E-02 0.5801992 at 110iterations 1.6786082E-02 0.3100102 at 120iterations 9.3611963E-03 0.2003632 at 130iterations 5.2218349E-03 9.4483376E-02 at 140iterations 2.9136450E-03 5.4878235E-02 at 150iterations 1.6295866E-03 3.1997681E-02 at 160iterations 9.1785856E-04 1.6460896E-02 at 170iterations 5.2165199E-04 9.3617439E-03 at 180iterations finished qdiffx linear iterations at : 17:56:03 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 5.2165199E-04 9.3617439E-03 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 17:56:04 16.340u 0.322s 0:16.92 98.4% 0+0k 0+0io 0pf+0w