Sun Oct 9 08:14:58 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 08:14:58 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4355167 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 0.4355167 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 527.3434 centred at (gu) : 91.58797 83.01846 89.87308 assigned negative charge : -515.8450 centred at (gu) : 91.63145 83.12041 89.81137 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4325 nv = 96 ne = 84 npr = 72798 no. pairs analyzed = 72798 no. exposed pairs = 4776 no. arc points = 35188 no. surface atoms = 1595 nbur = 2073 mkacc time = 0.1500000 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 = 1.932000 m= 109 mr = 1952 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2786 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 5671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2429076E-13 4.9591086E-12 midg,1,midg; midg,igrid,midg 6.1584175E-11 -1.4988935E-13 1,midg,midg; igrid,midg,midg 2.7629951E-12 1.4842530E-12 gauss-seidel spectral radius is 0.9730566 estimated iterations to convergence 51 setup time was (sec) 0.5900000 now iterating at: 08:14:58 rms-change max change #iterations 2.4025720E-02 5.099843 at 10iterations 1.0832291E-03 0.2354546 at 20iterations 1.7961825E-04 3.4072876E-02 at 30iterations 4.0227045E-05 7.8287125E-03 at 40iterations 9.1766333E-06 1.7908812E-03 at 50iterations finished qdiffx linear iterations at : 08:15:01 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 9.1766333E-06 1.7908812E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 08:15:01 3.233u 0.122s 0:03.63 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 08:15:01 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 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: 1.306550 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 1.306550 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 527.3434 centred at (gu) : 94.76296 69.05470 89.61833 assigned negative charge : -515.8450 centred at (gu) : 94.89393 69.36083 89.43345 start vw surface at 0.1800000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 49805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 11068 mr = 31695 m= 579 mr = 6482 m= 10 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1355 time to turn everything in is 0.4200000 number of dielectric boundary points 23154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 593 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 23768 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) : 0.4355167 object centre at (A) : -4.462501 18.59800 16.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4399802E-03 2.3737680E-03 midg,1,midg; midg,igrid,midg 1.5120869E-02 -2.8665501E-04 1,midg,midg; igrid,midg,midg 7.9946459E-04 3.9946393E-05 gauss-seidel spectral radius is 0.9971245 estimated iterations to convergence 149 setup time was (sec) 0.7200000 now iterating at: 08:15:02 rms-change max change #iterations 2.097780 138.5900 at 10iterations 0.7018737 45.41783 at 20iterations 0.2346910 12.02173 at 30iterations 7.7975519E-02 3.751236 at 40iterations 2.6078753E-02 1.119745 at 50iterations 8.6810421E-03 0.4632759 at 60iterations 2.9178583E-03 0.1563740 at 70iterations 9.9580013E-04 4.5899391E-02 at 80iterations 3.4891034E-04 1.6931534E-02 at 90iterations 1.3174553E-04 5.7296753E-03 at 100iterations 5.7218524E-05 2.4566650E-03 at 110iterations 2.8272181E-05 1.2302399E-03 at 120iterations finished qdiffx linear iterations at : 08:15:10 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 2.8272181E-05 1.2302399E-03 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 08:15:10 8.493u 0.203s 0:08.99 96.6% 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 08:15:10 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 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: 1.959825 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 1.959825 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 527.3434 centred at (gu) : 97.14426 58.58193 89.42736 assigned negative charge : -515.8450 centred at (gu) : 97.34088 59.04111 89.15021 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 116476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 43115 mr = 78891 m= 7604 mr = 31574 m= 589 mr = 4854 m= 7 mr = 230 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 4651 time to turn everything in is 0.8900000 number of dielectric boundary points 52240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26734 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) : 1.306550 object centre at (A) : -4.462501 18.59800 16.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0858973E-02 4.7156427E-02 midg,1,midg; midg,igrid,midg 0.4309545 1.2624336E-03 1,midg,midg; igrid,midg,midg 1.5487679E-02 -1.2493134E-02 gauss-seidel spectral radius is 0.9987326 estimated iterations to convergence 222 setup time was (sec) 1.210000 now iterating at: 08:15:12 rms-change max change #iterations 6.316651 276.2527 at 10iterations 3.181708 116.0377 at 20iterations 1.584263 54.02227 at 30iterations 0.7834397 27.85824 at 40iterations 0.3847458 13.13929 at 50iterations 0.1888642 6.036227 at 60iterations 9.2379406E-02 2.705311 at 70iterations 4.5122001E-02 1.326642 at 80iterations 2.1941178E-02 0.7373581 at 90iterations 1.0653299E-02 0.3497243 at 100iterations 5.1795281E-03 0.1584396 at 110iterations 2.5198625E-03 6.9294453E-02 at 120iterations 1.2226751E-03 3.7167072E-02 at 130iterations 5.9360528E-04 1.8333435E-02 at 140iterations 2.8819352E-04 8.4934235E-03 at 150iterations 1.4008337E-04 4.0397644E-03 at 160iterations 6.8109599E-05 1.7967224E-03 at 170iterations 3.3266708E-05 9.5748901E-04 at 180iterations finished qdiffx linear iterations at : 08:15:22 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 3.3266708E-05 9.5748901E-04 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 08:15:23 11.934u 0.273s 0:12.51 97.5% 0+0k 0+0io 0pf+0w