Sat Oct 8 16:47:34 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 Sat Oct 8 2011 at 16:47:35 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5466411 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): 16.54900 78.40000 ymin,ymax (A): 119.0010 184.1260 zmin,zma (A): -1.982000 55.17500 x,y,z range (A): 61.85100 65.12499 57.15700 scale (grids/A): 0.5466411 object centre (A): 47.47450 151.5635 26.59650 number of atom coordinates read : 4473 total number of charged atoms : 4307 net assigned charge : 2.500036 assigned positive charge : 692.0058 centred at (gu) : 91.93053 89.17645 88.30392 assigned negative charge : -689.5092 centred at (gu) : 91.88361 89.09412 88.32921 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8561 nv = 96 ne = 84 npr = 89494 no. pairs analyzed = 89494 no. exposed pairs = 5311 no. arc points = 37520 no. surface atoms = 1774 nbur = 2699 mkacc time = 0.1900000 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 = 1.568000 m= 361 mr = 4666 m= 0 mr = 26 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4200000 number of dielectric boundary points 4230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3865 ## 556 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3353922E-10 -7.3131980E-11 midg,1,midg; midg,igrid,midg -8.8863672E-10 8.1835599E-10 1,midg,midg; igrid,midg,midg -2.1020850E-10 1.0390786E-09 gauss-seidel spectral radius is 0.9828556 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 16:47:35 rms-change max change #iterations 9.5066711E-02 14.54235 at 10iterations 6.6015646E-03 0.9380646 at 20iterations 6.2220928E-04 9.1171265E-02 at 30iterations 1.2750593E-04 1.6461849E-02 at 40iterations 3.3960176E-05 4.6465397E-03 at 50iterations finished qdiffx linear iterations at : 16:47:38 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 3.3960176E-05 4.6465397E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 16:47:38 3.241u 0.157s 0:03.74 90.6% 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 Sat Oct 8 2011 at 16:47:38 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.639923 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): 16.54900 78.40000 ymin,ymax (A): 119.0010 184.1260 zmin,zma (A): -1.982000 55.17500 x,y,z range (A): 61.85100 65.12499 57.15700 scale (grids/A): 1.639923 object centre (A): 47.47450 151.5635 26.59650 number of atom coordinates read : 4473 total number of charged atoms : 4307 net assigned charge : 2.500036 assigned positive charge : 692.0058 centred at (gu) : 95.79057 87.52814 84.91084 assigned negative charge : -689.5092 centred at (gu) : 95.65043 87.28204 84.98711 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 96288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30332 mr = 67569 m= 3494 mr = 21372 m= 99 mr = 1957 m= 0 mr = 18 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1647 time to turn everything in is 0.6300000 number of dielectric boundary points 39297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 453 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 33016 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) : 0.5466411 object centre at (A) : 47.47450 151.5635 26.59650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8727654E-03 4.6164417E-03 midg,1,midg; midg,igrid,midg 1.4204924E-02 3.3157304E-02 1,midg,midg; igrid,midg,midg -1.0681387E-02 -1.6201355E-02 gauss-seidel spectral radius is 0.9983461 estimated iterations to convergence 195 setup time was (sec) 0.9100000 now iterating at: 16:47:39 rms-change max change #iterations 4.306562 260.3741 at 10iterations 1.862067 125.5755 at 20iterations 0.8060879 37.58407 at 30iterations 0.3503952 13.50604 at 40iterations 0.1520799 5.265799 at 50iterations 6.6284344E-02 2.244807 at 60iterations 2.8713565E-02 0.9965706 at 70iterations 1.2473258E-02 0.4169960 at 80iterations 5.4397415E-03 0.1661072 at 90iterations 2.3729047E-03 7.2313309E-02 at 100iterations 1.0396949E-03 3.1337738E-02 at 110iterations 4.5676206E-04 1.3122231E-02 at 120iterations finished qdiffx linear iterations at : 16:47:45 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 4.5676206E-04 1.3122231E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 16:47:46 7.210u 0.180s 0:07.68 96.2% 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 Sat Oct 8 2011 at 16:47:46 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.459885 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): 16.54900 78.40000 ymin,ymax (A): 119.0010 184.1260 zmin,zma (A): -1.982000 55.17500 x,y,z range (A): 61.85100 65.12499 57.15700 scale (grids/A): 2.459885 object centre (A): 47.47450 151.5635 26.59650 number of atom coordinates read : 4473 total number of charged atoms : 4307 net assigned charge : 2.500036 assigned positive charge : 692.0058 centred at (gu) : 98.68550 86.29194 82.36581 assigned negative charge : -689.5092 centred at (gu) : 98.47565 85.92307 82.48064 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 224225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 104927 mr = 165268 m= 30913 mr = 84111 m= 5738 mr = 23716 m= 495 mr = 4182 m= 11 mr = 289 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5368 time to turn everything in is 1.550000 number of dielectric boundary points 88743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 34433 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) : 1.639923 object centre at (A) : 47.47450 151.5635 26.59650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8149230E-02 9.6739970E-02 midg,1,midg; midg,igrid,midg 0.2343556 0.6178289 1,midg,midg; igrid,midg,midg -0.1552006 -0.3165673 gauss-seidel spectral radius is 0.9992161 estimated iterations to convergence 282 setup time was (sec) 1.840000 now iterating at: 16:47:48 rms-change max change #iterations 11.07725 409.2083 at 10iterations 6.400680 159.6312 at 20iterations 3.671191 85.52643 at 30iterations 2.101757 36.71840 at 40iterations 1.199483 24.37059 at 50iterations 0.6837665 11.19648 at 60iterations 0.3879378 6.836699 at 70iterations 0.2203372 4.133323 at 80iterations 0.1251398 2.218140 at 90iterations 7.0749246E-02 1.432552 at 100iterations 4.0042132E-02 0.6489325 at 110iterations 2.2703936E-02 0.3912034 at 120iterations 1.2858099E-02 0.2175709 at 130iterations 7.2651664E-03 0.1258955 at 140iterations 4.1083721E-03 7.1277618E-02 at 150iterations 2.3256564E-03 4.1629791E-02 at 160iterations 1.3148506E-03 2.3101807E-02 at 170iterations 7.4552017E-04 1.3120651E-02 at 180iterations finished qdiffx linear iterations at : 16:47:58 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 7.4552017E-04 1.3120651E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 16:47:59 11.877u 0.171s 0:12.53 96.0% 0+0k 0+0io 0pf+0w