Tue Oct 11 07:07:38 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+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 Tue Oct 11 2011 at 07:07:38 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5418322 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 0.5418322 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3615 net assigned charge : 9.420031 assigned positive charge : 573.5103 centred at (gu) : 90.04835 89.39095 90.76849 assigned negative charge : -564.0926 centred at (gu) : 90.03707 89.24002 90.81223 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 76110 no. pairs analyzed = 76110 no. exposed pairs = 4479 no. arc points = 30769 no. surface atoms = 1506 nbur = 2255 mkacc time = 0.1300000 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= 262 mr = 3952 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3140 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9338 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8105538E-10 2.2770943E-10 midg,1,midg; midg,igrid,midg -7.0503264E-10 1.3543764E-09 1,midg,midg; igrid,midg,midg 4.2248646E-10 5.9695454E-10 gauss-seidel spectral radius is 0.9824951 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 07:07:39 rms-change max change #iterations 7.9243928E-02 14.04200 at 10iterations 6.1029624E-03 0.9008541 at 20iterations 9.8988344E-04 0.1916809 at 30iterations 2.8103331E-04 5.6446075E-02 at 40iterations 8.4170002E-05 1.6899109E-02 at 50iterations finished qdiffx linear iterations at : 07:07:41 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 8.4170002E-05 1.6899109E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:07:42 3.424u 0.171s 0:04.37 82.1% 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 Tue Oct 11 2011 at 07:07:42 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.625497 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 1.625497 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3615 net assigned charge : 9.420031 assigned positive charge : 573.5103 centred at (gu) : 90.14404 88.17151 92.30400 assigned negative charge : -564.0926 centred at (gu) : 90.11063 87.71952 92.43633 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25788 mr = 55691 m= 2598 mr = 18714 m= 51 mr = 1340 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 0.3800000 number of dielectric boundary points 31650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 385 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 27661 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) : 0.5418322 object centre at (A) : 22.18050 -6.056000 92.73801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9735398E-03 -1.2352833E-03 midg,1,midg; midg,igrid,midg -1.2993182E-02 1.3431496E-02 1,midg,midg; igrid,midg,midg 1.7279387E-02 9.2164455E-03 gauss-seidel spectral radius is 0.9982455 estimated iterations to convergence 190 setup time was (sec) 0.5900000 now iterating at: 07:07:43 rms-change max change #iterations 3.808619 159.3536 at 10iterations 1.605481 59.66428 at 20iterations 0.6831540 23.21196 at 30iterations 0.2897943 9.183517 at 40iterations 0.1231195 4.434613 at 50iterations 5.2267008E-02 1.796447 at 60iterations 2.2311263E-02 0.8123980 at 70iterations 9.5427046E-03 0.3139915 at 80iterations 4.1280813E-03 0.1459389 at 90iterations 1.8413985E-03 7.0121765E-02 at 100iterations 8.5269928E-04 3.2470703E-02 at 110iterations 4.1830781E-04 1.7614365E-02 at 120iterations finished qdiffx linear iterations at : 07:07:50 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 4.1830781E-04 1.7614365E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 07:07:51 7.721u 0.200s 0:08.37 94.6% 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 Tue Oct 11 2011 at 07:07:51 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.438245 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 2.438245 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3615 net assigned charge : 9.420031 assigned positive charge : 573.5103 centred at (gu) : 90.21559 87.25700 93.45578 assigned negative charge : -564.0926 centred at (gu) : 90.16597 86.57917 93.65427 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88136 mr = 135385 m= 26425 mr = 71799 m= 4044 mr = 20794 m= 208 mr = 2734 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2727 time to turn everything in is 0.9700000 number of dielectric boundary points 71434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 28878 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) : 1.625497 object centre at (A) : 22.18050 -6.056000 92.73801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7541302E-02 -5.8285248E-02 midg,1,midg; midg,igrid,midg -0.1371524 0.1625120 1,midg,midg; igrid,midg,midg 0.2740931 -0.2135907 gauss-seidel spectral radius is 0.9991702 estimated iterations to convergence 274 setup time was (sec) 1.210000 now iterating at: 07:07:52 rms-change max change #iterations 9.592032 429.9829 at 10iterations 5.402123 141.2069 at 20iterations 3.020834 64.12967 at 30iterations 1.687988 32.83635 at 40iterations 0.9424189 18.67487 at 50iterations 0.5243514 10.39975 at 60iterations 0.2926833 5.334230 at 70iterations 0.1628772 3.113191 at 80iterations 9.0630084E-02 1.709973 at 90iterations 5.0524764E-02 1.035427 at 100iterations 2.8027877E-02 0.5782433 at 110iterations 1.5649972E-02 0.2992496 at 120iterations 8.7034171E-03 0.1711559 at 130iterations 4.8720664E-03 0.1069965 at 140iterations 2.7454826E-03 5.5088043E-02 at 150iterations 1.5572731E-03 3.0349731E-02 at 160iterations 8.9570897E-04 1.7960548E-02 at 170iterations 5.2957889E-04 1.2357712E-02 at 180iterations finished qdiffx linear iterations at : 07:08:03 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 5.2957889E-04 1.2357712E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 07:08:04 12.535u 0.182s 0:13.06 97.3% 0+0k 0+0io 0pf+0w