Sat Oct 15 10:22:41 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 15 2011 at 10:22:41 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 = 4260 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: 0.5822797 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 0.5822797 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 640.3063 centred at (gu) : 91.02647 88.83749 88.36117 assigned negative charge : -642.3094 centred at (gu) : 90.87349 88.99551 88.55575 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9350 nv = 96 ne = 84 npr = 88891 no. pairs analyzed = 88891 no. exposed pairs = 4908 no. arc points = 32850 no. surface atoms = 1680 nbur = 2580 mkacc time = 0.1900000 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 = 1.484000 m= 393 mr = 5407 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.4300000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3519 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5859400E-09 -5.1112492E-09 midg,1,midg; midg,igrid,midg 6.0684644E-09 -4.7219779E-09 1,midg,midg; igrid,midg,midg -4.7348245E-09 5.6606697E-09 gauss-seidel spectral radius is 0.9848688 estimated iterations to convergence 67 setup time was (sec) 0.7000000 now iterating at: 10:22:42 rms-change max change #iterations 0.1212118 14.66761 at 10iterations 1.0740896E-02 1.459202 at 20iterations 1.8983296E-03 0.2816544 at 30iterations 6.0381170E-04 7.1983337E-02 at 40iterations 2.1971119E-04 2.3662567E-02 at 50iterations finished qdiffx linear iterations at : 10:22:46 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 2.1971119E-04 2.3662567E-02 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 10:22:47 4.511u 0.318s 0:05.39 89.4% 0+0k 0+0io 6pf+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 15 2011 at 10:22:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4260 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: 1.746839 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 1.746839 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 640.3063 centred at (gu) : 93.07813 86.51133 85.08253 assigned negative charge : -642.3094 centred at (gu) : 92.61986 86.98648 85.66691 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 103805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32850 grid for indexing accessible points = 1.400000 m= 36115 mr = 75547 m= 4765 mr = 26655 m= 180 mr = 2832 m= 0 mr = 26 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3797 time to turn everything in is 0.7600000 number of dielectric boundary points 39805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 31939 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) : 0.5822797 object centre at (A) : 4.899499 65.59850 61.19800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8330700E-02 -3.2190859E-02 midg,1,midg; midg,igrid,midg 2.9580368E-02 -4.9213201E-02 1,midg,midg; igrid,midg,midg -1.3771664E-02 3.8390592E-02 gauss-seidel spectral radius is 0.9985318 estimated iterations to convergence 207 setup time was (sec) 1.150000 now iterating at: 10:22:48 rms-change max change #iterations 4.741914 175.5074 at 10iterations 2.153283 65.72478 at 20iterations 0.9808043 27.99062 at 30iterations 0.4483779 12.53446 at 40iterations 0.2049900 6.372593 at 50iterations 9.3738511E-02 2.526720 at 60iterations 4.2957038E-02 1.289334 at 70iterations 1.9795811E-02 0.5451260 at 80iterations 9.1794953E-03 0.2564926 at 90iterations 4.3431795E-03 0.1187878 at 100iterations 2.1313687E-03 6.5872192E-02 at 110iterations 1.1096224E-03 3.3370972E-02 at 120iterations finished qdiffx linear iterations at : 10:22:58 total time elapsed so far: 10.56000 # loops : 120 mean,max change (kT/e) : 1.1096224E-03 3.3370972E-02 energy calculations done at 10.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 10:22:58 10.741u 0.317s 0:11.38 97.1% 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 Sat Oct 15 2011 at 10:22:58 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 = 4260 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: 2.620259 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 2.620259 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 640.3063 centred at (gu) : 94.61682 84.76653 82.62349 assigned negative charge : -642.3094 centred at (gu) : 93.92975 85.47955 83.50022 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 241270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32850 grid for indexing accessible points = 1.400000 m= 121202 mr = 183153 m= 39455 mr = 100017 m= 8125 mr = 31219 m= 830 mr = 5976 m= 23 mr = 503 m= 0 mr = 5 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 12520 time to turn everything in is 1.990000 number of dielectric boundary points 90032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 32870 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) : 1.746839 object centre at (A) : 4.899499 65.59850 61.19800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.011852 -0.3723525 midg,1,midg; midg,igrid,midg 0.3920741 -1.048460 1,midg,midg; igrid,midg,midg -7.6237604E-02 0.2936480 gauss-seidel spectral radius is 0.9992573 estimated iterations to convergence 290 setup time was (sec) 2.390000 now iterating at: 10:23:01 rms-change max change #iterations 11.56090 372.1349 at 10iterations 6.813923 140.4810 at 20iterations 3.966223 71.11855 at 30iterations 2.309519 38.32318 at 40iterations 1.338081 24.85523 at 50iterations 0.7740866 12.88316 at 60iterations 0.4476829 8.368262 at 70iterations 0.2577663 4.167495 at 80iterations 0.1490575 2.387810 at 90iterations 8.5790999E-02 1.453417 at 100iterations 4.9463499E-02 0.7832756 at 110iterations 2.8466024E-02 0.4251850 at 120iterations 1.6449166E-02 0.2597094 at 130iterations 9.5149996E-03 0.1439009 at 140iterations 5.5355467E-03 8.9952469E-02 at 150iterations 3.2553086E-03 5.6423187E-02 at 160iterations 1.9465283E-03 3.3874512E-02 at 170iterations 1.1979727E-03 1.9973755E-02 at 180iterations finished qdiffx linear iterations at : 10:23:16 total time elapsed so far: 17.72000 # loops : 180 mean,max change (kT/e) : 1.1979727E-03 1.9973755E-02 energy calculations done at 17.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.90000 DelPhi exited at 10:23:17 17.901u 0.356s 0:18.82 96.9% 0+0k 0+0io 0pf+0w