Mon Oct 10 17:01:24 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 Mon Oct 10 2011 at 17:01:24 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 = 2772 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: 0.6264738 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 0.6264738 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.499979 assigned positive charge : 413.0733 centred at (gu) : 89.01633 89.56096 88.87602 assigned negative charge : -416.5743 centred at (gu) : 88.96388 89.48381 88.79187 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 55586 no. pairs analyzed = 55586 no. exposed pairs = 3657 no. arc points = 25723 no. surface atoms = 1241 nbur = 1531 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3816 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2200000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3474172E-08 3.0120333E-09 midg,1,midg; midg,igrid,midg -1.0908244E-08 2.9923835E-09 1,midg,midg; igrid,midg,midg -9.6224975E-09 9.5725894E-10 gauss-seidel spectral radius is 0.9868255 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 17:01:25 rms-change max change #iterations 0.1324492 18.86993 at 10iterations 1.2425365E-02 1.990354 at 20iterations 1.1754978E-03 0.1647453 at 30iterations 1.0992172E-04 1.4862061E-02 at 40iterations 1.0395868E-05 1.5888214E-03 at 50iterations finished qdiffx linear iterations at : 17:01:28 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.0395868E-05 1.5888214E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:01:28 3.553u 0.197s 0:04.15 90.1% 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 Mon Oct 10 2011 at 17:01:28 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 = 2772 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: 1.879421 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 1.879421 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.499979 assigned positive charge : 413.0733 centred at (gu) : 87.04831 88.68249 86.62720 assigned negative charge : -416.5743 centred at (gu) : 86.89139 88.45119 86.37540 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25723 grid for indexing accessible points = 1.400000 m= 26735 mr = 54279 m= 3599 mr = 18832 m= 175 mr = 1960 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.3800000 number of dielectric boundary points 35369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20671 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) : 0.6264738 object centre at (A) : 42.42200 59.11800 89.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4974358E-04 1.5973719E-02 midg,1,midg; midg,igrid,midg -1.9500211E-02 -4.2434703E-03 1,midg,midg; igrid,midg,midg -5.1900871E-02 2.2142440E-02 gauss-seidel spectral radius is 0.9986228 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 17:01:29 rms-change max change #iterations 4.281186 189.4730 at 10iterations 1.987101 66.94518 at 20iterations 0.9275908 28.58777 at 30iterations 0.4320194 14.36635 at 40iterations 0.2010251 6.303814 at 50iterations 9.4048314E-02 3.014651 at 60iterations 4.3788292E-02 1.282745 at 70iterations 2.0423455E-02 0.6533041 at 80iterations 9.5435865E-03 0.3292575 at 90iterations 4.4496083E-03 0.1306946 at 100iterations 2.0777269E-03 6.5811157E-02 at 110iterations 9.6625159E-04 3.3237457E-02 at 120iterations finished qdiffx linear iterations at : 17:01:37 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 9.6625159E-04 3.3237457E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 17:01:39 8.228u 0.237s 0:10.41 81.1% 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 Mon Oct 10 2011 at 17:01:39 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 = 2772 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: 2.819132 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 2.819132 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.499979 assigned positive charge : 413.0733 centred at (gu) : 85.57220 88.02348 84.94078 assigned negative charge : -416.5743 centred at (gu) : 85.33695 87.67660 84.56299 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25723 grid for indexing accessible points = 1.400000 m= 88698 mr = 132470 m= 29296 mr = 70922 m= 6148 mr = 22556 m= 727 mr = 4302 m= 30 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 5287 time to turn everything in is 1.010000 number of dielectric boundary points 79651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 21051 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) : 1.879421 object centre at (A) : 42.42200 59.11800 89.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2127327 0.1484615 midg,1,midg; midg,igrid,midg -0.1946903 -8.2531445E-02 1,midg,midg; igrid,midg,midg -0.6712401 0.2470957 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.270000 now iterating at: 17:01:40 rms-change max change #iterations 10.32792 388.3603 at 10iterations 6.148775 151.7585 at 20iterations 3.626296 79.96796 at 30iterations 2.125007 47.30427 at 40iterations 1.243221 26.94981 at 50iterations 0.7246495 16.51426 at 60iterations 0.4227357 9.316769 at 70iterations 0.2450213 5.607916 at 80iterations 0.1424174 2.865063 at 90iterations 8.2344316E-02 1.705347 at 100iterations 4.7676593E-02 0.9405863 at 110iterations 2.7609149E-02 0.5481758 at 120iterations 1.5961073E-02 0.3082795 at 130iterations 9.2342366E-03 0.1702423 at 140iterations 5.3245369E-03 0.1050439 at 150iterations 3.0846901E-03 5.8507442E-02 at 160iterations 1.7796081E-03 3.5675049E-02 at 170iterations 1.0313899E-03 2.0776749E-02 at 180iterations finished qdiffx linear iterations at : 17:01:52 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 1.0313899E-03 2.0776749E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 17:01:53 13.449u 0.236s 0:14.36 95.1% 0+0k 0+0io 0pf+0w