Tue Oct 11 03:25:36 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 Tue Oct 11 2011 at 03:25:36 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 = 2541 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: 0.5755768 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 0.5755768 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2396 net assigned charge : 5.500023 assigned positive charge : 381.2440 centred at (gu) : 92.57973 91.35468 90.44582 assigned negative charge : -375.7447 centred at (gu) : 92.63458 91.35097 90.48177 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 50898 no. pairs analyzed = 50898 no. exposed pairs = 3264 no. arc points = 23264 no. surface atoms = 1099 nbur = 1442 mkacc time = 0.1100000 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 = 1.484000 m= 222 mr = 2864 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 2899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2359 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4557128E-09 5.2050703E-10 midg,1,midg; midg,igrid,midg 7.2666650E-10 1.5110826E-09 1,midg,midg; igrid,midg,midg 1.0554791E-09 2.5894198E-10 gauss-seidel spectral radius is 0.9843867 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 03:25:37 rms-change max change #iterations 8.8834278E-02 15.44685 at 10iterations 6.7037838E-03 1.070999 at 20iterations 5.1590684E-04 8.3883286E-02 at 30iterations 4.4136366E-05 7.6343417E-03 at 40iterations 5.6136860E-06 1.1024475E-03 at 50iterations finished qdiffx linear iterations at : 03:25:39 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 5.6136860E-06 1.1024475E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:25:40 3.295u 0.183s 0:04.11 84.4% 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 03:25:40 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 = 2541 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: 1.726730 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 1.726730 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2396 net assigned charge : 5.500023 assigned positive charge : 381.2440 centred at (gu) : 97.73893 94.06364 91.33678 assigned negative charge : -375.7447 centred at (gu) : 97.90338 94.05282 91.44510 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 19001 mr = 40486 m= 2207 mr = 13138 m= 87 mr = 1262 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1123 time to turn everything in is 0.4400000 number of dielectric boundary points 26919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 18580 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) : 0.5755768 object centre at (A) : 7.562000 69.57850 9.293499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9418992E-03 1.1506618E-02 midg,1,midg; midg,igrid,midg -1.1829891E-02 -9.2745163E-03 1,midg,midg; igrid,midg,midg 5.0766760E-04 5.9802260E-04 gauss-seidel spectral radius is 0.9983329 estimated iterations to convergence 194 setup time was (sec) 0.7300000 now iterating at: 03:25:41 rms-change max change #iterations 3.392962 146.1088 at 10iterations 1.460662 65.79890 at 20iterations 0.6315479 24.61920 at 30iterations 0.2725068 10.13143 at 40iterations 0.1176075 4.600807 at 50iterations 5.0865311E-02 1.836240 at 60iterations 2.1956623E-02 0.8377876 at 70iterations 9.4991140E-03 0.3612604 at 80iterations 4.1066301E-03 0.1543713 at 90iterations 1.7746609E-03 7.0881844E-02 at 100iterations 7.7063229E-04 3.1760693E-02 at 110iterations 3.3263379E-04 1.2685061E-02 at 120iterations finished qdiffx linear iterations at : 03:25:47 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 3.3263379E-04 1.2685061E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 03:25:48 7.301u 0.211s 0:07.83 95.9% 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 03:25:48 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 = 2541 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: 2.590096 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 2.590096 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2396 net assigned charge : 5.500023 assigned positive charge : 381.2440 centred at (gu) : 101.6081 96.09533 92.00499 assigned negative charge : -375.7447 centred at (gu) : 101.8551 96.07918 92.16761 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 140369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 64998 mr = 99176 m= 19321 mr = 51299 m= 3543 mr = 14667 m= 376 mr = 2544 m= 5 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 3587 time to turn everything in is 1.030000 number of dielectric boundary points 60685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 19157 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) : 1.726730 object centre at (A) : 7.562000 69.57850 9.293499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0711665E-02 0.2007398 midg,1,midg; midg,igrid,midg -0.1989832 -0.1449043 1,midg,midg; igrid,midg,midg -2.6989786E-02 2.3806815E-03 gauss-seidel spectral radius is 0.9991732 estimated iterations to convergence 275 setup time was (sec) 1.340000 now iterating at: 03:25:50 rms-change max change #iterations 8.519077 283.9345 at 10iterations 4.843884 117.3978 at 20iterations 2.724319 64.97490 at 30iterations 1.528781 36.36228 at 40iterations 0.8581462 20.12774 at 50iterations 0.4798566 10.71134 at 60iterations 0.2677339 6.134109 at 70iterations 0.1492718 3.034176 at 80iterations 8.3284155E-02 1.772095 at 90iterations 4.6424136E-02 1.027744 at 100iterations 2.5850210E-02 0.5867176 at 110iterations 1.4406548E-02 0.3311615 at 120iterations 8.0109490E-03 0.1713562 at 130iterations 4.4581951E-03 9.1119766E-02 at 140iterations 2.4806759E-03 5.5418968E-02 at 150iterations 1.3817867E-03 2.8162956E-02 at 160iterations 7.7039126E-04 1.6481400E-02 at 170iterations 4.2859835E-04 9.1419220E-03 at 180iterations finished qdiffx linear iterations at : 03:26:00 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 4.2859835E-04 9.1419220E-03 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 03:26:00 11.724u 0.240s 0:12.27 97.4% 0+0k 0+0io 0pf+0w