Mon Oct 10 10:08:18 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 10:08:18 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 = 2721 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: 0.5815948 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 0.5815948 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.000013 assigned positive charge : 393.1273 centred at (gu) : 88.53141 88.23035 87.44914 assigned negative charge : -387.1275 centred at (gu) : 88.59136 88.05939 87.38247 start vw surface at 2.600000 fill in re-entrant regions at 2.610000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 52504 no. pairs analyzed = 52504 no. exposed pairs = 4168 no. arc points = 30358 no. surface atoms = 1388 nbur = 1333 mkacc time = 0.1400001 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= 294 mr = 2651 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.800000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2919 ## 312 charges are in solution ## iepsmp to db, and charging done at 2.910000 number of grid points assigned charge 7800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4331784E-10 1.5481785E-09 midg,1,midg; midg,igrid,midg -3.1289624E-09 3.1781036E-09 1,midg,midg; igrid,midg,midg 3.7214338E-09 1.9711366E-10 gauss-seidel spectral radius is 0.9847388 estimated iterations to convergence 66 setup time was (sec) 3.080000 now iterating at: 10:08:22 rms-change max change #iterations 9.0621457E-02 14.76687 at 10iterations 7.1753580E-03 1.230795 at 20iterations 5.6318904E-04 0.1178284 at 30iterations 5.1367660E-05 9.7846985E-03 at 40iterations 6.7120004E-06 1.4171600E-03 at 50iterations finished qdiffx linear iterations at : 10:08:26 total time elapsed so far: 7.010000 # loops : 50 mean,max change (kT/e) : 6.7120004E-06 1.4171600E-03 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 10:08:27 7.190u 0.455s 0:08.90 85.8% 0+0k 0+0io 9pf+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 10:08:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 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: 1.744784 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 1.744784 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.000013 assigned positive charge : 393.1273 centred at (gu) : 85.59396 84.69081 82.34728 assigned negative charge : -387.1275 centred at (gu) : 85.77406 84.17805 82.14735 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30358 grid for indexing accessible points = 1.400000 m= 20869 mr = 39722 m= 2697 mr = 13165 m= 91 mr = 1333 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 35571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19990 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) : 0.5815948 object centre at (A) : 7.773499 -30.20050 29.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6304173E-02 3.4731098E-03 midg,1,midg; midg,igrid,midg 1.8576028E-02 3.2823931E-02 1,midg,midg; igrid,midg,midg 1.2182729E-02 5.0336332E-03 gauss-seidel spectral radius is 0.9984125 estimated iterations to convergence 199 setup time was (sec) 0.9300000 now iterating at: 10:08:29 rms-change max change #iterations 3.568980 174.6427 at 10iterations 1.571381 60.85743 at 20iterations 0.6904975 23.47758 at 30iterations 0.3033486 10.66615 at 40iterations 0.1347204 4.685327 at 50iterations 5.9006564E-02 2.528929 at 60iterations 2.6077481E-02 0.8661716 at 70iterations 1.1477000E-02 0.3883839 at 80iterations 5.0451751E-03 0.1790047 at 90iterations 2.2341984E-03 8.0268860E-02 at 100iterations 9.8451786E-04 4.1516304E-02 at 110iterations 4.3410150E-04 1.6478300E-02 at 120iterations finished qdiffx linear iterations at : 10:08:39 total time elapsed so far: 10.95000 # loops : 120 mean,max change (kT/e) : 4.3410150E-04 1.6478300E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 10:08:39 11.134u 0.480s 0:12.74 91.1% 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 Mon Oct 10 2011 at 10:08:40 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 = 2721 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: 2.617177 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 2.617177 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.000013 assigned positive charge : 393.1273 centred at (gu) : 83.39090 82.03614 78.52081 assigned negative charge : -387.1275 centred at (gu) : 83.66097 81.26707 78.22089 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30358 grid for indexing accessible points = 1.400000 m= 67668 mr = 98321 m= 22326 mr = 50028 m= 4437 mr = 16136 m= 363 mr = 2780 m= 9 mr = 162 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 80288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20573 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) : 1.744784 object centre at (A) : 7.773499 -30.20050 29.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4380300 4.2606689E-02 midg,1,midg; midg,igrid,midg 0.3366449 0.4024619 1,midg,midg; igrid,midg,midg 4.5541447E-02 5.7685759E-02 gauss-seidel spectral radius is 0.9992250 estimated iterations to convergence 284 setup time was (sec) 1.810000 now iterating at: 10:08:42 rms-change max change #iterations 9.094969 310.6526 at 10iterations 5.385914 154.4137 at 20iterations 3.138794 73.41438 at 30iterations 1.815942 45.07230 at 40iterations 1.046669 27.02533 at 50iterations 0.6029178 13.81224 at 60iterations 0.3456680 7.834158 at 70iterations 0.1973909 4.317752 at 80iterations 0.1124099 3.153463 at 90iterations 6.4025171E-02 1.679529 at 100iterations 3.6443174E-02 0.8029900 at 110iterations 2.0697875E-02 0.4227371 at 120iterations 1.1775349E-02 0.2620583 at 130iterations 6.6980026E-03 0.1321640 at 140iterations 3.7883201E-03 8.3207846E-02 at 150iterations 2.1510611E-03 4.2352676E-02 at 160iterations 1.2174801E-03 2.8409958E-02 at 170iterations 6.9287990E-04 1.4600277E-02 at 180iterations finished qdiffx linear iterations at : 10:08:59 total time elapsed so far: 19.14000 # loops : 180 mean,max change (kT/e) : 6.9287990E-04 1.4600277E-02 energy calculations done at 19.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.31000 DelPhi exited at 10:09:00 19.318u 0.536s 0:20.14 98.5% 0+0k 0+0io 0pf+0w