Sun Oct 9 11:54:15 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 Sun Oct 9 2011 at 11:54:15 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 = 2661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6595035 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): -6.169000 47.78400 ymin,ymax (A): 8.868000 61.05500 zmin,zma (A): 6.179000 60.15900 x,y,z range (A): 53.95300 52.18700 53.98000 scale (grids/A): 0.6595035 object centre (A): 20.80750 34.96150 33.16900 number of atom coordinates read : 2661 total number of charged atoms : 2591 net assigned charge : 1.000013 assigned positive charge : 397.2682 centred at (gu) : 90.76681 89.81726 91.15398 assigned negative charge : -396.2697 centred at (gu) : 90.82988 89.77810 91.07336 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8355 nv = 96 ne = 84 npr = 50369 no. pairs analyzed = 50369 no. exposed pairs = 3849 no. arc points = 27386 no. surface atoms = 1273 nbur = 1388 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 538 mr = 4256 m= 0 mr = 76 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2565 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9647 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0762383E-08 2.3447717E-08 midg,1,midg; midg,igrid,midg -5.6223848E-09 9.8135509E-09 1,midg,midg; igrid,midg,midg 1.2694833E-08 -1.2062268E-08 gauss-seidel spectral radius is 0.9881133 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 11:54:16 rms-change max change #iterations 0.1642856 22.48642 at 10iterations 1.7542157E-02 2.311419 at 20iterations 1.8413692E-03 0.2406530 at 30iterations 1.9626082E-04 2.3169041E-02 at 40iterations 2.1209635E-05 3.3378601E-03 at 50iterations finished qdiffx linear iterations at : 11:54:19 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.1209635E-05 3.3378601E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:54:19 3.412u 0.173s 0:03.88 92.2% 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 11:54:19 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 = 2661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.978511 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): -6.169000 47.78400 ymin,ymax (A): 8.868000 61.05500 zmin,zma (A): 6.179000 60.15900 x,y,z range (A): 53.95300 52.18700 53.98000 scale (grids/A): 1.978511 object centre (A): 20.80750 34.96150 33.16900 number of atom coordinates read : 2661 total number of charged atoms : 2591 net assigned charge : 1.000013 assigned positive charge : 397.2682 centred at (gu) : 92.29956 89.45086 93.46078 assigned negative charge : -396.2697 centred at (gu) : 92.48978 89.33428 93.22003 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 88410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27386 grid for indexing accessible points = 1.400000 m= 32474 mr = 58412 m= 6378 mr = 23082 m= 570 mr = 4104 m= 9 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.4200000 number of dielectric boundary points 41976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20499 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) : 0.6595035 object centre at (A) : 20.80750 34.96150 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3102360E-03 3.0046569E-02 midg,1,midg; midg,igrid,midg -3.5770878E-03 2.8112227E-02 1,midg,midg; igrid,midg,midg -2.0108443E-02 -7.0142285E-03 gauss-seidel spectral radius is 0.9987717 estimated iterations to convergence 226 setup time was (sec) 0.6400000 now iterating at: 11:54:20 rms-change max change #iterations 4.628488 193.7590 at 10iterations 2.248307 80.68504 at 20iterations 1.090581 34.83270 at 30iterations 0.5306439 15.99340 at 40iterations 0.2581136 7.875954 at 50iterations 0.1251354 3.539692 at 60iterations 6.0728882E-02 1.755310 at 70iterations 2.9411023E-02 0.8833365 at 80iterations 1.4353220E-02 0.4003730 at 90iterations 7.0132152E-03 0.2126768 at 100iterations 3.4050404E-03 0.1046524 at 110iterations 1.6550740E-03 4.6100974E-02 at 120iterations finished qdiffx linear iterations at : 11:54:27 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.6550740E-03 4.6100974E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 11:54:28 8.034u 0.217s 0:08.57 96.1% 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 Sun Oct 9 2011 at 11:54:28 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 = 2661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.967766 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): -6.169000 47.78400 ymin,ymax (A): 8.868000 61.05500 zmin,zma (A): 6.179000 60.15900 x,y,z range (A): 53.95300 52.18700 53.98000 scale (grids/A): 2.967766 object centre (A): 20.80750 34.96150 33.16900 number of atom coordinates read : 2661 total number of charged atoms : 2591 net assigned charge : 1.000013 assigned positive charge : 397.2682 centred at (gu) : 93.44901 89.17624 95.19109 assigned negative charge : -396.2697 centred at (gu) : 93.73463 89.00150 94.82993 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 203841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27386 grid for indexing accessible points = 1.400000 m= 101691 mr = 142398 m= 40174 mr = 80485 m= 11902 mr = 31813 m= 2427 mr = 8954 m= 235 mr = 1767 m= 7 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1714 time to turn everything in is 1.130000 number of dielectric boundary points 94752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20728 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) : 1.978511 object centre at (A) : 20.80750 34.96150 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1871875E-02 0.3715360 midg,1,midg; midg,igrid,midg 3.9855681E-02 0.2790090 1,midg,midg; igrid,midg,midg -0.2607154 0.2572048 gauss-seidel spectral radius is 0.9993240 estimated iterations to convergence 303 setup time was (sec) 1.380000 now iterating at: 11:54:29 rms-change max change #iterations 11.02613 392.2394 at 10iterations 6.700705 171.8947 at 20iterations 4.059929 99.18788 at 30iterations 2.440524 55.32554 at 40iterations 1.467601 36.36265 at 50iterations 0.8767257 18.37197 at 60iterations 0.5221974 10.92506 at 70iterations 0.3108004 6.105586 at 80iterations 0.1844648 3.284071 at 90iterations 0.1093971 2.313606 at 100iterations 6.4790510E-02 1.220014 at 110iterations 3.8379762E-02 0.7018299 at 120iterations 2.2644280E-02 0.4518881 at 130iterations 1.3418266E-02 0.2314774 at 140iterations 7.9240836E-03 0.1297646 at 150iterations 4.6868399E-03 8.8452339E-02 at 160iterations 2.7648145E-03 4.7255039E-02 at 170iterations 1.6323768E-03 2.8654099E-02 at 180iterations finished qdiffx linear iterations at : 11:54:41 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.6323768E-03 2.8654099E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 11:54:41 13.086u 0.221s 0:13.72 96.9% 0+0k 0+0io 0pf+0w