Tue Oct 11 04:22:42 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 04:22:42 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 79 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6495520 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 0.6495520 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4859830 assigned positive charge : 411.3479 centred at (gu) : 90.03387 90.17757 91.99924 assigned negative charge : -411.8344 centred at (gu) : 89.77753 89.99480 91.94643 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7457 nv = 96 ne = 84 npr = 55997 no. pairs analyzed = 55997 no. exposed pairs = 3174 no. arc points = 21832 no. surface atoms = 1072 nbur = 1617 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4340 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3600000 number of dielectric boundary points 3513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2588206E-09 1.1277469E-08 midg,1,midg; midg,igrid,midg -2.9644655E-08 2.8533281E-08 1,midg,midg; igrid,midg,midg -4.2775099E-08 3.8923950E-08 gauss-seidel spectral radius is 0.9877197 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 04:22:44 rms-change max change #iterations 0.1636281 25.37428 at 10iterations 1.7055243E-02 2.243635 at 20iterations 2.0398060E-03 0.2654800 at 30iterations 3.2760040E-04 5.3756714E-02 at 40iterations 8.1270184E-05 1.1726379E-02 at 50iterations finished qdiffx linear iterations at : 04:22:46 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 8.1270184E-05 1.1726379E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:22:47 3.118u 0.156s 0:04.22 77.2% 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 Tue Oct 11 2011 at 04:22:47 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 79 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.948656 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 1.948656 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4859830 assigned positive charge : 411.3479 centred at (gu) : 90.10126 90.53208 95.99694 assigned negative charge : -411.8344 centred at (gu) : 89.33237 89.98423 95.83926 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21832 grid for indexing accessible points = 1.400000 m= 30668 mr = 57780 m= 4937 mr = 23263 m= 296 mr = 3235 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2425 time to turn everything in is 0.5500000 number of dielectric boundary points 32463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20005 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) : 0.6495520 object centre at (A) : 12.71750 -1.457500 17.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5294973E-02 -4.4304617E-03 midg,1,midg; midg,igrid,midg -3.4461755E-02 2.8437693E-02 1,midg,midg; igrid,midg,midg -2.5826586E-02 4.7469791E-02 gauss-seidel spectral radius is 0.9986979 estimated iterations to convergence 220 setup time was (sec) 0.8100000 now iterating at: 04:22:48 rms-change max change #iterations 4.606361 182.1319 at 10iterations 2.205024 72.68182 at 20iterations 1.053514 31.65092 at 30iterations 0.5037295 15.97000 at 40iterations 0.2421929 8.231083 at 50iterations 0.1153270 3.471260 at 60iterations 5.5324193E-02 1.674891 at 70iterations 2.6394581E-02 0.8621941 at 80iterations 1.2766740E-02 0.4108276 at 90iterations 6.1846878E-03 0.1765499 at 100iterations 3.0242954E-03 9.5352173E-02 at 110iterations 1.5350891E-03 4.7115326E-02 at 120iterations finished qdiffx linear iterations at : 04:22:54 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 1.5350891E-03 4.7115326E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 04:22:54 6.911u 0.158s 0:07.56 93.3% 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 Tue Oct 11 2011 at 04:22:54 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 79 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.922984 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 2.922984 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4859830 assigned positive charge : 411.3479 centred at (gu) : 90.15178 90.79798 98.99535 assigned negative charge : -411.8344 centred at (gu) : 88.99846 89.97618 98.75868 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 187244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21832 grid for indexing accessible points = 1.400000 m= 98554 mr = 139327 m= 36651 mr = 82155 m= 9047 mr = 30207 m= 1391 mr = 7007 m= 98 mr = 987 m= 0 mr = 45 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 8078 time to turn everything in is 1.390000 number of dielectric boundary points 73257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 20319 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) : 1.948656 object centre at (A) : 12.71750 -1.457500 17.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4139307 7.3908694E-02 midg,1,midg; midg,igrid,midg -0.3935692 0.3505186 1,midg,midg; igrid,midg,midg -0.1873419 0.3872123 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 04:22:56 rms-change max change #iterations 10.64367 497.6406 at 10iterations 6.231108 145.1805 at 20iterations 3.633474 74.72919 at 30iterations 2.117214 40.08030 at 40iterations 1.230955 23.39041 at 50iterations 0.7139021 13.80345 at 60iterations 0.4150035 7.378132 at 70iterations 0.2401776 4.237675 at 80iterations 0.1392208 2.550411 at 90iterations 8.0555394E-02 1.400977 at 100iterations 4.6799932E-02 0.8298416 at 110iterations 2.7245406E-02 0.4859767 at 120iterations 1.5950628E-02 0.3080235 at 130iterations 9.4544403E-03 0.1668110 at 140iterations 5.7088430E-03 0.1038666 at 150iterations 3.5637841E-03 7.3371887E-02 at 160iterations 2.3327998E-03 4.8748016E-02 at 170iterations 1.6234054E-03 3.4435272E-02 at 180iterations finished qdiffx linear iterations at : 04:23:07 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 1.6234054E-03 3.4435272E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 04:23:08 12.727u 0.176s 0:13.19 97.7% 0+0k 0+0io 0pf+0w