Tue Oct 11 04:19:17 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 04:19:17 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 = 2689 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: 0.6991221 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): -10.57700 36.76900 ymin,ymax (A): 6.750000 55.76200 zmin,zma (A): -5.199000 45.72200 x,y,z range (A): 47.34600 49.01200 50.92100 scale (grids/A): 0.6991221 object centre (A): 13.09600 31.25600 20.26150 number of atom coordinates read : 2689 total number of charged atoms : 2543 net assigned charge : 5.500024 assigned positive charge : 410.0326 centred at (gu) : 89.73431 90.68348 90.88484 assigned negative charge : -404.5334 centred at (gu) : 89.48021 90.54346 91.01168 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8947 nv = 96 ne = 84 npr = 54432 no. pairs analyzed = 54432 no. exposed pairs = 3371 no. arc points = 23474 no. surface atoms = 1124 nbur = 1565 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 596 mr = 5148 m= 8 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.2000000 number of dielectric boundary points 4305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2187 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 10079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8464084E-08 -3.5676184E-08 midg,1,midg; midg,igrid,midg -3.1613659E-08 1.2835595E-07 1,midg,midg; igrid,midg,midg -1.0523178E-07 1.6150346E-07 gauss-seidel spectral radius is 0.9893972 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 04:19:18 rms-change max change #iterations 0.2170133 25.72275 at 10iterations 2.6204458E-02 3.645645 at 20iterations 3.2241950E-03 0.3820133 at 30iterations 4.0577209E-04 5.1368713E-02 at 40iterations 5.9337857E-05 7.2326660E-03 at 50iterations finished qdiffx linear iterations at : 04:19:21 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.9337857E-05 7.2326660E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 04:19:21 3.396u 0.193s 0:04.00 89.5% 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 04:19:21 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 = 2689 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: 2.097366 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): -10.57700 36.76900 ymin,ymax (A): 6.750000 55.76200 zmin,zma (A): -5.199000 45.72200 x,y,z range (A): 47.34600 49.01200 50.92100 scale (grids/A): 2.097366 object centre (A): 13.09600 31.25600 20.26150 number of atom coordinates read : 2689 total number of charged atoms : 2543 net assigned charge : 5.500024 assigned positive charge : 410.0326 centred at (gu) : 89.20231 92.04977 92.65379 assigned negative charge : -404.5334 centred at (gu) : 88.44029 91.62994 93.03469 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 94208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23474 grid for indexing accessible points = 1.400000 m= 38996 mr = 66700 m= 7796 mr = 29857 m= 662 mr = 5277 m= 14 mr = 299 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1824 time to turn everything in is 0.4700000 number of dielectric boundary points 39541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 20172 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) : 0.6991221 object centre at (A) : 13.09600 31.25600 20.26150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1209056E-02 8.7385792E-03 midg,1,midg; midg,igrid,midg -9.0506533E-03 5.9763927E-02 1,midg,midg; igrid,midg,midg -2.9432995E-02 8.7319516E-02 gauss-seidel spectral radius is 0.9988691 estimated iterations to convergence 235 setup time was (sec) 0.6800000 now iterating at: 04:19:22 rms-change max change #iterations 5.257688 207.4979 at 10iterations 2.625451 102.9354 at 20iterations 1.321853 40.32423 at 30iterations 0.6619694 19.92401 at 40iterations 0.3331226 8.544704 at 50iterations 0.1672823 4.335656 at 60iterations 8.4149875E-02 2.438880 at 70iterations 4.2264532E-02 1.257389 at 80iterations 2.1229874E-02 0.5722380 at 90iterations 1.0662790E-02 0.3100084 at 100iterations 5.3649298E-03 0.1417599 at 110iterations 2.6996175E-03 6.9984436E-02 at 120iterations finished qdiffx linear iterations at : 04:19:29 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 2.6996175E-03 6.9984436E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 04:19:30 8.027u 0.233s 0:08.89 92.8% 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 Tue Oct 11 2011 at 04:19:30 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 = 2689 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: 3.146050 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): -10.57700 36.76900 ymin,ymax (A): 6.750000 55.76200 zmin,zma (A): -5.199000 45.72200 x,y,z range (A): 47.34600 49.01200 50.92100 scale (grids/A): 3.146050 object centre (A): 13.09600 31.25600 20.26150 number of atom coordinates read : 2689 total number of charged atoms : 2543 net assigned charge : 5.500024 assigned positive charge : 410.0326 centred at (gu) : 88.80338 93.07451 93.98069 assigned negative charge : -404.5334 centred at (gu) : 87.66057 92.44493 94.55197 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 217219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23474 grid for indexing accessible points = 1.400000 m= 119488 mr = 160454 m= 50916 mr = 99721 m= 14684 mr = 42243 m= 2779 mr = 11515 m= 263 mr = 1953 m= 12 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 6400 time to turn everything in is 1.450000 number of dielectric boundary points 89335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 20340 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) : 2.097366 object centre at (A) : 13.09600 31.25600 20.26150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6943542 0.3801823 midg,1,midg; midg,igrid,midg -0.1044727 0.6492792 1,midg,midg; igrid,midg,midg -0.2150859 0.6674570 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 1.680000 now iterating at: 04:19:32 rms-change max change #iterations 11.56630 396.6154 at 10iterations 6.856741 124.3272 at 20iterations 4.067155 76.74431 at 30iterations 2.403564 44.69913 at 40iterations 1.417217 23.08980 at 50iterations 0.8393364 14.57820 at 60iterations 0.4943999 8.010941 at 70iterations 0.2912215 5.124750 at 80iterations 0.1710975 2.946295 at 90iterations 0.1009618 1.541744 at 100iterations 5.9292533E-02 0.9759445 at 110iterations 3.4884445E-02 0.5716743 at 120iterations 2.0547302E-02 0.3350697 at 130iterations 1.2116025E-02 0.2324001 at 140iterations 7.1696672E-03 0.1119375 at 150iterations 4.2646485E-03 6.9059849E-02 at 160iterations 2.5602516E-03 4.4433594E-02 at 170iterations 1.5565306E-03 2.6748657E-02 at 180iterations finished qdiffx linear iterations at : 04:19:44 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 1.5565306E-03 2.6748657E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 04:19:44 13.353u 0.232s 0:13.93 97.4% 0+0k 0+0io 0pf+0w