Sun Oct 9 14:46:29 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 14:46:29 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 = 3116 !!! WARNING: ASP 287 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5309708 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 0.5309708 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 467.0767 centred at (gu) : 90.20992 90.35503 90.08942 assigned negative charge : -471.5780 centred at (gu) : 90.11026 90.23751 90.08921 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5846 nv = 96 ne = 84 npr = 60041 no. pairs analyzed = 60041 no. exposed pairs = 4655 no. arc points = 33683 no. surface atoms = 1511 nbur = 1605 mkacc time = 0.1400000 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 = 1.596000 m= 261 mr = 2622 m= 1 mr = 14 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 0.3700000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3246 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7695 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5303304E-10 -1.5820494E-10 midg,1,midg; midg,igrid,midg -5.7393990E-10 3.3284775E-10 1,midg,midg; igrid,midg,midg -5.2663901E-10 2.4768496E-10 gauss-seidel spectral radius is 0.9817476 estimated iterations to convergence 61 setup time was (sec) 0.5900000 now iterating at: 14:46:30 rms-change max change #iterations 6.3902624E-02 10.87417 at 10iterations 3.8930494E-03 0.7620277 at 20iterations 2.8316129E-04 4.6310425E-02 at 30iterations 4.8154016E-05 6.0181618E-03 at 40iterations 1.4311135E-05 1.6489029E-03 at 50iterations finished qdiffx linear iterations at : 14:46:32 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.4311135E-05 1.6489029E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:46:33 3.384u 0.147s 0:03.83 91.9% 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 14:46:33 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 = 3116 !!! WARNING: ASP 287 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.592913 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 1.592913 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 467.0767 centred at (gu) : 90.62914 91.06413 90.26732 assigned negative charge : -471.5780 centred at (gu) : 90.33051 90.71225 90.26722 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19042 mr = 39882 m= 2072 mr = 11636 m= 64 mr = 798 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.5100000 number of dielectric boundary points 32521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 401 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22568 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) : 0.5309708 object centre at (A) : 40.18950 -2.048500 1.9500732E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2177046E-02 -9.8407490E-04 midg,1,midg; midg,igrid,midg -5.9972294E-03 2.5864388E-03 1,midg,midg; igrid,midg,midg -9.5599042E-03 5.4568489E-04 gauss-seidel spectral radius is 0.9981279 estimated iterations to convergence 184 setup time was (sec) 0.7900000 now iterating at: 14:46:34 rms-change max change #iterations 3.250155 154.2693 at 10iterations 1.325964 48.31284 at 20iterations 0.5427184 20.41148 at 30iterations 0.2223477 7.992476 at 40iterations 9.1246493E-02 3.569919 at 50iterations 3.7448496E-02 1.510845 at 60iterations 1.5373656E-02 0.7216797 at 70iterations 6.3006263E-03 0.2319458 at 80iterations 2.5952589E-03 9.9701405E-02 at 90iterations 1.0721660E-03 3.7642479E-02 at 100iterations 4.4689598E-04 1.6572714E-02 at 110iterations 1.8814184E-04 6.8211555E-03 at 120iterations finished qdiffx linear iterations at : 14:46:40 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.8814184E-04 6.8211555E-03 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 14:46:41 7.436u 0.176s 0:07.88 96.4% 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 Sun Oct 9 2011 at 14:46:41 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 = 3116 !!! WARNING: ASP 287 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.389369 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 2.389369 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 467.0767 centred at (gu) : 90.94328 91.59587 90.40087 assigned negative charge : -471.5780 centred at (gu) : 90.49564 91.06830 90.40067 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 147789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65494 mr = 99009 m= 17999 mr = 48323 m= 3064 mr = 11972 m= 231 mr = 1657 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 1.170000 number of dielectric boundary points 73551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 23710 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) : 1.592913 object centre at (A) : 40.18950 -2.048500 1.9500732E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.055952 6.5920852E-02 midg,1,midg; midg,igrid,midg -9.8004609E-02 4.9758568E-02 1,midg,midg; igrid,midg,midg -0.1065442 -1.6856544E-02 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.470000 now iterating at: 14:46:42 rms-change max change #iterations 8.821353 301.2297 at 10iterations 5.067647 153.4086 at 20iterations 2.892451 85.63967 at 30iterations 1.631017 45.39575 at 40iterations 0.9172421 32.07333 at 50iterations 0.5112819 13.48261 at 60iterations 0.2851363 7.141691 at 70iterations 0.1583850 4.070404 at 80iterations 8.8002890E-02 2.517685 at 90iterations 4.8674878E-02 1.225159 at 100iterations 2.7022829E-02 0.7183399 at 110iterations 1.4905948E-02 0.3587818 at 120iterations 8.2374252E-03 0.1865116 at 130iterations 4.5442828E-03 0.1148434 at 140iterations 2.5109923E-03 5.7271659E-02 at 150iterations 1.3802203E-03 3.3597946E-02 at 160iterations 7.6303061E-04 1.8150330E-02 at 170iterations 4.2046871E-04 9.3479156E-03 at 180iterations finished qdiffx linear iterations at : 14:46:53 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 4.2046871E-04 9.3479156E-03 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 14:46:53 11.827u 0.182s 0:12.28 97.7% 0+0k 0+0io 0pf+0w