Mon Oct 10 19:32:33 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 Mon Oct 10 2011 at 19:32:33 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2519 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6451846 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): -9.398000 42.22200 ymin,ymax (A): -12.16900 40.33900 zmin,zma (A): -10.76800 44.41000 x,y,z range (A): 51.62000 52.50800 55.17800 scale (grids/A): 0.6451846 object centre (A): 16.41200 14.08500 16.82100 number of atom coordinates read : 2519 total number of charged atoms : 2384 net assigned charge : -2.499988 assigned positive charge : 372.9749 centred at (gu) : 89.78432 88.53052 89.73740 assigned negative charge : -375.4760 centred at (gu) : 89.78300 88.60056 89.81554 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7269 nv = 96 ne = 84 npr = 50535 no. pairs analyzed = 50535 no. exposed pairs = 3437 no. arc points = 24063 no. surface atoms = 1149 nbur = 1370 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3854 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2314 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8456 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0043353E-09 -1.3802189E-08 midg,1,midg; midg,igrid,midg 6.4797767E-09 -9.9191935E-09 1,midg,midg; igrid,midg,midg -4.7611537E-09 -4.0301904E-09 gauss-seidel spectral radius is 0.9875568 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 19:32:34 rms-change max change #iterations 0.1485997 22.57768 at 10iterations 1.5239853E-02 2.177664 at 20iterations 1.6541854E-03 0.2172518 at 30iterations 2.2996039E-04 3.3630371E-02 at 40iterations 4.8799971E-05 7.0819855E-03 at 50iterations finished qdiffx linear iterations at : 19:32:37 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 4.8799971E-05 7.0819855E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:32:38 3.429u 0.162s 0:04.43 80.8% 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 19:32:38 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2519 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.935554 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): -9.398000 42.22200 ymin,ymax (A): -12.16900 40.33900 zmin,zma (A): -10.76800 44.41000 x,y,z range (A): 51.62000 52.50800 55.17800 scale (grids/A): 1.935554 object centre (A): 16.41200 14.08500 16.82100 number of atom coordinates read : 2519 total number of charged atoms : 2384 net assigned charge : -2.499988 assigned positive charge : 372.9749 centred at (gu) : 89.35246 85.59092 89.21164 assigned negative charge : -375.4760 centred at (gu) : 89.34893 85.80157 89.44681 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24063 grid for indexing accessible points = 1.400000 m= 27716 mr = 52424 m= 4654 mr = 19990 m= 353 mr = 2908 m= 6 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 362 time to turn everything in is 0.4100000 number of dielectric boundary points 35044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18808 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) : 0.6451846 object centre at (A) : 16.41200 14.08500 16.82100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9287702E-03 -6.2778071E-02 midg,1,midg; midg,igrid,midg 5.4507870E-02 -5.1698275E-04 1,midg,midg; igrid,midg,midg -7.8164354E-05 6.6081728E-03 gauss-seidel spectral radius is 0.9986861 estimated iterations to convergence 219 setup time was (sec) 0.6300000 now iterating at: 19:32:38 rms-change max change #iterations 4.316133 212.1788 at 10iterations 2.041369 76.26201 at 20iterations 0.9621028 30.75148 at 30iterations 0.4589676 15.12775 at 40iterations 0.2177035 6.864397 at 50iterations 0.1029680 3.409452 at 60iterations 4.8999108E-02 1.552370 at 70iterations 2.3326047E-02 0.7586241 at 80iterations 1.1063208E-02 0.3244667 at 90iterations 5.2862791E-03 0.1594124 at 100iterations 2.5236027E-03 7.7411652E-02 at 110iterations 1.2076600E-03 3.3588409E-02 at 120iterations finished qdiffx linear iterations at : 19:32:46 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.2076600E-03 3.3588409E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 19:32:46 7.914u 0.196s 0:08.41 96.3% 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 19:32:46 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2519 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.903331 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): -9.398000 42.22200 ymin,ymax (A): -12.16900 40.33900 zmin,zma (A): -10.76800 44.41000 x,y,z range (A): 51.62000 52.50800 55.17800 scale (grids/A): 2.903331 object centre (A): 16.41200 14.08500 16.82100 number of atom coordinates read : 2519 total number of charged atoms : 2384 net assigned charge : -2.499988 assigned positive charge : 372.9749 centred at (gu) : 89.02853 83.38625 88.81732 assigned negative charge : -375.4760 centred at (gu) : 89.02338 83.70231 89.17027 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24063 grid for indexing accessible points = 1.400000 m= 88787 mr = 127313 m= 32760 mr = 71437 m= 8438 mr = 26054 m= 1363 mr = 6320 m= 126 mr = 920 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 1203 time to turn everything in is 1.010000 number of dielectric boundary points 79275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19067 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) : 1.935554 object centre at (A) : 16.41200 14.08500 16.82100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1224496 -0.7012050 midg,1,midg; midg,igrid,midg 0.9130039 1.1301740E-02 1,midg,midg; igrid,midg,midg -7.6624565E-02 9.2731163E-02 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.250000 now iterating at: 19:32:48 rms-change max change #iterations 10.14835 368.9084 at 10iterations 5.972689 157.0081 at 20iterations 3.509651 72.44054 at 30iterations 2.044367 46.22758 at 40iterations 1.190869 23.05807 at 50iterations 0.6942100 13.40530 at 60iterations 0.4028104 7.178066 at 70iterations 0.2339731 4.075344 at 80iterations 0.1356508 2.991568 at 90iterations 7.8716837E-02 1.407860 at 100iterations 4.5646109E-02 0.8295193 at 110iterations 2.6497735E-02 0.4814243 at 120iterations 1.5339636E-02 0.2582474 at 130iterations 8.9041432E-03 0.1645584 at 140iterations 5.1767435E-03 9.2117310E-02 at 150iterations 3.0211008E-03 5.0632477E-02 at 160iterations 1.7731419E-03 3.0361414E-02 at 170iterations 1.0541935E-03 2.0829916E-02 at 180iterations finished qdiffx linear iterations at : 19:32:59 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.0541935E-03 2.0829916E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 19:33:00 12.898u 0.222s 0:13.71 95.6% 0+0k 0+0io 0pf+0w