Wed Dec 21 14:21:26 PST 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 Wed Dec 21 2011 at 14:21:27 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5740269 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): -34.93800 10.09800 ymin,ymax (A): 1.529000 41.66900 zmin,zma (A): -4.745000 57.27300 x,y,z range (A): 45.03600 40.14000 62.01800 scale (grids/A): 0.5740269 object centre (A): -12.42000 21.59900 26.26400 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 2.000005 assigned positive charge : 292.5259 centred at (gu) : 90.28001 89.46091 90.88400 assigned negative charge : -290.5262 centred at (gu) : 90.19484 89.59921 90.88298 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4382 nv = 96 ne = 84 npr = 39529 no. pairs analyzed = 39529 no. exposed pairs = 2477 no. arc points = 17353 no. surface atoms = 845 nbur = 1121 mkacc time = 6.0000002E-02 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 = 1.512000 m= 182 mr = 2339 m= 0 mr = 23 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1812 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5470 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7054636E-10 4.3454690E-10 midg,1,midg; midg,igrid,midg 2.2119351E-09 -1.1519381E-09 1,midg,midg; igrid,midg,midg -6.2591876E-10 1.4272578E-09 gauss-seidel spectral radius is 0.9842569 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 14:21:28 rms-change max change #iterations 7.4166127E-02 13.81555 at 10iterations 5.6407102E-03 1.033402 at 20iterations 4.1798691E-04 8.6295128E-02 at 30iterations 3.2019954E-05 5.9013367E-03 at 40iterations 2.3982959E-06 4.8065186E-04 at 50iterations finished qdiffx linear iterations at : 14:21:31 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 2.3982959E-06 4.8065186E-04 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:21:42 3.768u 0.260s 0:15.22 26.4% 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 Wed Dec 21 2011 at 14:21:44 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.722081 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): -34.93800 10.09800 ymin,ymax (A): 1.529000 41.66900 zmin,zma (A): -4.745000 57.27300 x,y,z range (A): 45.03600 40.14000 62.01800 scale (grids/A): 1.722081 object centre (A): -12.42000 21.59900 26.26400 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 2.000005 assigned positive charge : 292.5259 centred at (gu) : 90.83978 88.38271 92.65203 assigned negative charge : -290.5262 centred at (gu) : 90.58467 88.79805 92.64914 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 47702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 16163 mr = 32590 m= 1987 mr = 11881 m= 62 mr = 1175 m= 0 mr = 11 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 20257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14209 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) : 0.5740269 object centre at (A) : -12.42000 21.59900 26.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5891708E-02 2.3048429E-02 midg,1,midg; midg,igrid,midg -9.6452591E-04 -6.6322624E-03 1,midg,midg; igrid,midg,midg -1.4237558E-03 -6.0589256E-04 gauss-seidel spectral radius is 0.9982542 estimated iterations to convergence 190 setup time was (sec) 0.5100000 now iterating at: 14:21:45 rms-change max change #iterations 2.949820 151.7258 at 10iterations 1.241507 54.08413 at 20iterations 0.5274740 22.93563 at 30iterations 0.2230399 9.833654 at 40iterations 9.4699182E-02 3.799794 at 50iterations 4.0374815E-02 1.884686 at 60iterations 1.7013490E-02 0.6981303 at 70iterations 7.2299843E-03 0.2872896 at 80iterations 3.0751384E-03 0.1330931 at 90iterations 1.3007278E-03 5.4846287E-02 at 100iterations 5.5209809E-04 2.2638321E-02 at 110iterations 2.3406553E-04 9.5748901E-03 at 120iterations finished qdiffx linear iterations at : 14:21:54 total time elapsed so far: 9.000000 # loops : 120 mean,max change (kT/e) : 2.3406553E-04 9.5748901E-03 energy calculations done at 9.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.140000 DelPhi exited at 14:22:14 9.143u 0.313s 0:30.99 30.4% 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 Wed Dec 21 2011 at 14:22:16 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.583121 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): -34.93800 10.09800 ymin,ymax (A): 1.529000 41.66900 zmin,zma (A): -4.745000 57.27300 x,y,z range (A): 45.03600 40.14000 62.01800 scale (grids/A): 2.583121 object centre (A): -12.42000 21.59900 26.26400 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 2.000005 assigned positive charge : 292.5259 centred at (gu) : 91.25966 87.57418 93.97793 assigned negative charge : -290.5262 centred at (gu) : 90.87696 88.19704 93.97376 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 110316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 54218 mr = 78987 m= 17326 mr = 44191 m= 3302 mr = 13921 m= 312 mr = 2466 m= 4 mr = 196 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 45715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14667 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) : 1.722081 object centre at (A) : -12.42000 21.59900 26.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1595961 0.2689484 midg,1,midg; midg,igrid,midg -5.6963451E-02 -8.7277830E-02 1,midg,midg; igrid,midg,midg -2.7455725E-02 -3.2481600E-02 gauss-seidel spectral radius is 0.9991258 estimated iterations to convergence 267 setup time was (sec) 0.8300000 now iterating at: 14:22:18 rms-change max change #iterations 7.358177 363.5009 at 10iterations 4.098125 119.6716 at 20iterations 2.256175 54.83681 at 30iterations 1.240023 27.95621 at 40iterations 0.6834590 16.52770 at 50iterations 0.3732289 8.579472 at 60iterations 0.2036909 4.706402 at 70iterations 0.1114626 2.577889 at 80iterations 6.0968887E-02 1.339018 at 90iterations 3.3436403E-02 0.8093987 at 100iterations 1.8226447E-02 0.4308701 at 110iterations 9.9688359E-03 0.2309244 at 120iterations 5.4344339E-03 0.1498499 at 130iterations 2.9738210E-03 6.8506241E-02 at 140iterations 1.6275757E-03 3.8165808E-02 at 150iterations 8.8812638E-04 2.1043777E-02 at 160iterations 4.8496432E-04 1.0476589E-02 at 170iterations 2.6481246E-04 5.5859089E-03 at 180iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 2.6481246E-04 5.5859089E-03 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 14:22:42 13.440u 0.250s 0:25.75 53.1% 0+0k 0+0io 0pf+0w