Sun Oct 9 23:34:29 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 Sun Oct 9 2011 at 23:34:29 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 = 2433 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: 0.6006513 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 0.6006513 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2372 net assigned charge : 2.000006 assigned positive charge : 376.1871 centred at (gu) : 89.17802 90.17870 88.17163 assigned negative charge : -374.1878 centred at (gu) : 89.05990 90.23206 88.16154 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5716 nv = 96 ne = 84 npr = 47913 no. pairs analyzed = 47913 no. exposed pairs = 3090 no. arc points = 21991 no. surface atoms = 1037 nbur = 1396 mkacc time = 9.9999994E-02 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 = 1.456000 m= 246 mr = 3010 m= 0 mr = 16 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2600000 number of dielectric boundary points 2936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2235 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3508700E-10 8.5831103E-10 midg,1,midg; midg,igrid,midg 2.7076423E-09 -1.0377998E-09 1,midg,midg; igrid,midg,midg -4.0703361E-09 4.2195589E-09 gauss-seidel spectral radius is 0.9856392 estimated iterations to convergence 68 setup time was (sec) 0.4800000 now iterating at: 23:34:30 rms-change max change #iterations 0.1037470 17.74869 at 10iterations 8.6902296E-03 1.738614 at 20iterations 7.2975055E-04 0.1185484 at 30iterations 6.3275067E-05 9.8533630E-03 at 40iterations 5.4650009E-06 9.7656250E-04 at 50iterations finished qdiffx linear iterations at : 23:34:32 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 5.4650009E-06 9.7656250E-04 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 23:34:33 3.080u 0.144s 0:03.56 90.4% 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 Sun Oct 9 2011 at 23:34:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 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: 1.801954 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 1.801954 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2372 net assigned charge : 2.000006 assigned positive charge : 376.1871 centred at (gu) : 87.53369 90.53550 84.51411 assigned negative charge : -374.1878 centred at (gu) : 87.17954 90.69622 84.48457 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21991 grid for indexing accessible points = 1.400000 m= 20342 mr = 42090 m= 2484 mr = 14598 m= 103 mr = 1421 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1282 time to turn everything in is 0.4300000 number of dielectric boundary points 27261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18502 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) : 0.6006513 object centre at (A) : 21.92350 -0.5714998 15.79350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8625963E-02 2.6341020E-03 midg,1,midg; midg,igrid,midg -2.0179318E-03 -1.1313756E-03 1,midg,midg; igrid,midg,midg -2.9560423E-02 3.3528555E-02 gauss-seidel spectral radius is 0.9984549 estimated iterations to convergence 202 setup time was (sec) 0.7000000 now iterating at: 23:34:34 rms-change max change #iterations 3.706009 173.8655 at 10iterations 1.644660 71.14127 at 20iterations 0.7348658 24.79251 at 30iterations 0.3272395 12.19299 at 40iterations 0.1456971 5.314820 at 50iterations 6.4780779E-02 2.114802 at 60iterations 2.8972784E-02 1.023006 at 70iterations 1.2882879E-02 0.4567757 at 80iterations 5.7535195E-03 0.1996689 at 90iterations 2.5710235E-03 0.1049719 at 100iterations 1.1434088E-03 4.2203903E-02 at 110iterations 5.0897937E-04 2.1093369E-02 at 120iterations finished qdiffx linear iterations at : 23:34:40 total time elapsed so far: 6.560000 # loops : 120 mean,max change (kT/e) : 5.0897937E-04 2.1093369E-02 energy calculations done at 6.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 23:34:40 6.730u 0.147s 0:07.17 95.8% 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 Sun Oct 9 2011 at 23:34:40 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 = 2433 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: 2.702931 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 2.702931 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2372 net assigned charge : 2.000006 assigned positive charge : 376.1871 centred at (gu) : 86.30053 90.80312 81.77115 assigned negative charge : -374.1878 centred at (gu) : 85.76931 91.04431 81.72694 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 144674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21991 grid for indexing accessible points = 1.400000 m= 68201 mr = 102652 m= 21643 mr = 54713 m= 4230 mr = 16959 m= 421 mr = 3046 m= 13 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 4141 time to turn everything in is 1.040000 number of dielectric boundary points 61543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 18966 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) : 1.801954 object centre at (A) : 21.92350 -0.5714998 15.79350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2399666 3.1612221E-02 midg,1,midg; midg,igrid,midg -4.1320913E-02 3.3568718E-02 1,midg,midg; igrid,midg,midg -0.5123866 0.4098226 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 1.340000 now iterating at: 23:34:42 rms-change max change #iterations 8.878893 288.7547 at 10iterations 5.049026 125.7363 at 20iterations 2.851876 60.08224 at 30iterations 1.606919 35.05370 at 40iterations 0.9053324 18.61010 at 50iterations 0.5092539 10.66880 at 60iterations 0.2867202 5.633863 at 70iterations 0.1611851 3.246269 at 80iterations 9.0574428E-02 1.992257 at 90iterations 5.0996132E-02 1.122382 at 100iterations 2.8639736E-02 0.5695934 at 110iterations 1.6092759E-02 0.3173180 at 120iterations 9.0670129E-03 0.2026181 at 130iterations 5.1012435E-03 0.1043625 at 140iterations 2.8685441E-03 5.8384895E-02 at 150iterations 1.6184389E-03 3.3443272E-02 at 160iterations 9.0574485E-04 1.7905712E-02 at 170iterations 5.1049388E-04 1.1180162E-02 at 180iterations finished qdiffx linear iterations at : 23:34:51 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 5.1049388E-04 1.1180162E-02 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 23:34:52 10.951u 0.179s 0:11.41 97.4% 0+0k 0+0io 0pf+0w