Mon Oct 10 17:04:47 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 Mon Oct 10 2011 at 17:04:47 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 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: 0.5623924 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 0.5623924 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.00013 assigned positive charge : 636.7452 centred at (gu) : 91.01608 91.42341 88.95769 assigned negative charge : -588.7490 centred at (gu) : 90.96976 91.38341 89.03151 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8429 nv = 96 ne = 84 npr = 70863 no. pairs analyzed = 70863 no. exposed pairs = 6286 no. arc points = 46629 no. surface atoms = 2049 nbur = 1993 mkacc time = 0.2100000 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 = 1.540000 m= 374 mr = 3311 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 5485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4775 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10866 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5567278E-09 3.4167351E-09 midg,1,midg; midg,igrid,midg 3.5195891E-09 8.6182235E-09 1,midg,midg; igrid,midg,midg 3.7838346E-09 7.9494535E-09 gauss-seidel spectral radius is 0.9838037 estimated iterations to convergence 65 setup time was (sec) 0.7400000 now iterating at: 17:04:48 rms-change max change #iterations 9.7403638E-02 15.42665 at 10iterations 7.4022114E-03 1.145756 at 20iterations 9.7046967E-04 0.1096725 at 30iterations 2.4914381E-04 1.6431808E-02 at 40iterations 7.2525574E-05 4.2686462E-03 at 50iterations finished qdiffx linear iterations at : 17:04:51 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 7.2525574E-05 4.2686462E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 17:04:52 4.193u 0.266s 0:04.98 89.3% 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 Mon Oct 10 2011 at 17:04:52 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 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: 1.687177 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 1.687177 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.00013 assigned positive charge : 636.7452 centred at (gu) : 93.04716 94.26879 86.87138 assigned negative charge : -588.7490 centred at (gu) : 92.90916 94.15007 87.09438 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 90078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46629 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24888 mr = 51267 m= 2582 mr = 14496 m= 104 mr = 972 m= 0 mr = 8 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 50909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 30124 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) : 0.5623924 object centre at (A) : -11.78300 44.74150 58.16450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1080809E-02 2.4473032E-02 midg,1,midg; midg,igrid,midg 3.6031712E-02 7.4549139E-02 1,midg,midg; igrid,midg,midg 4.4307232E-02 0.1064064 gauss-seidel spectral radius is 0.9984571 estimated iterations to convergence 202 setup time was (sec) 1.100000 now iterating at: 17:04:53 rms-change max change #iterations 4.228519 148.3049 at 10iterations 1.873340 61.31009 at 20iterations 0.8361743 25.72102 at 30iterations 0.3725740 12.68855 at 40iterations 0.1660714 5.508076 at 50iterations 7.4061744E-02 2.660231 at 60iterations 3.3023592E-02 1.029539 at 70iterations 1.4746579E-02 0.4826946 at 80iterations 6.6264262E-03 0.2175375 at 90iterations 2.9826253E-03 0.1041756 at 100iterations 1.3505820E-03 4.6722412E-02 at 110iterations 6.1564473E-04 1.9653320E-02 at 120iterations finished qdiffx linear iterations at : 17:05:02 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 6.1564473E-04 1.9653320E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 17:05:03 9.799u 0.295s 0:10.91 92.3% 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 Mon Oct 10 2011 at 17:05:03 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 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: 2.530766 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 2.530766 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.00013 assigned positive charge : 636.7452 centred at (gu) : 94.57040 96.40301 85.30684 assigned negative charge : -588.7490 centred at (gu) : 94.36370 96.22512 85.64150 start vw surface at 0.2000000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 207981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46629 grid for indexing accessible points = 1.400000 m= 84573 mr = 127680 m= 23506 mr = 59967 m= 3809 mr = 15575 m= 289 mr = 2003 m= 6 mr = 94 m= 0 mr = 4 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 114841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 31296 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) : 1.687177 object centre at (A) : -11.78300 44.74150 58.16450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.020114 0.3750345 midg,1,midg; midg,igrid,midg 0.6032344 0.8312035 1,midg,midg; igrid,midg,midg 0.3403508 1.469158 gauss-seidel spectral radius is 0.9992903 estimated iterations to convergence 296 setup time was (sec) 2.270000 now iterating at: 17:05:06 rms-change max change #iterations 11.17624 307.2180 at 10iterations 6.808260 175.8829 at 20iterations 4.120302 108.5626 at 30iterations 2.473957 61.20644 at 40iterations 1.472367 30.97988 at 50iterations 0.8755479 19.71731 at 60iterations 0.5170150 12.33436 at 70iterations 0.3061871 6.616365 at 80iterations 0.1805318 3.629875 at 90iterations 0.1063543 2.276523 at 100iterations 6.2446289E-02 1.112875 at 110iterations 3.6582418E-02 0.8035703 at 120iterations 2.1453232E-02 0.3881826 at 130iterations 1.2555205E-02 0.2354126 at 140iterations 7.3386310E-03 0.1433344 at 150iterations 4.3007075E-03 8.0773354E-02 at 160iterations 2.5115826E-03 4.5333862E-02 at 170iterations 1.4650655E-03 2.5318146E-02 at 180iterations finished qdiffx linear iterations at : 17:05:20 total time elapsed so far: 16.79000 # loops : 180 mean,max change (kT/e) : 1.4650655E-03 2.5318146E-02 energy calculations done at 16.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.97000 DelPhi exited at 17:05:21 16.967u 0.313s 0:17.64 97.9% 0+0k 0+0io 0pf+0w