Sat Oct 15 14:59:29 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+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 Sat Oct 15 2011 at 14:59:29 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 has a net charge of 0.5140 !!! WARNING: MET 254 has a net charge of -0.2720 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: 0.5929183 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 0.5929183 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.256012 assigned positive charge : 399.4456 centred at (gu) : 90.09804 90.77002 87.52125 assigned negative charge : -394.1907 centred at (gu) : 90.10870 90.75945 87.41823 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6121 nv = 96 ne = 84 npr = 54314 no. pairs analyzed = 54314 no. exposed pairs = 3609 no. arc points = 25179 no. surface atoms = 1206 nbur = 1483 mkacc time = 0.1300000 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= 295 mr = 3025 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2593 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2859199E-09 2.7694660E-09 midg,1,midg; midg,igrid,midg 1.3019541E-09 2.5732487E-09 1,midg,midg; igrid,midg,midg 2.1192972E-09 1.5722260E-09 gauss-seidel spectral radius is 0.9852920 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 14:59:30 rms-change max change #iterations 0.1043022 18.29599 at 10iterations 8.6841453E-03 1.482856 at 20iterations 7.1753119E-04 0.1063423 at 30iterations 6.0804294E-05 9.7351074E-03 at 40iterations 5.7757084E-06 8.5449219E-04 at 50iterations finished qdiffx linear iterations at : 14:59:32 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.7757084E-06 8.5449219E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:59:33 3.436u 0.145s 0:03.88 92.0% 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 15 2011 at 14:59:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 has a net charge of 0.5140 !!! WARNING: MET 254 has a net charge of -0.2720 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: 1.778755 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 1.778755 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.256012 assigned positive charge : 399.4456 centred at (gu) : 90.29350 92.30933 82.56321 assigned negative charge : -394.1907 centred at (gu) : 90.32603 92.27827 82.25464 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25179 grid for indexing accessible points = 1.400000 m= 21248 mr = 43546 m= 2925 mr = 14393 m= 140 mr = 1559 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.5200000 number of dielectric boundary points 31121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19917 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) : 0.5929183 object centre at (A) : 1.108000 -3.728000 9.682002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7369263E-02 3.0835340E-02 midg,1,midg; midg,igrid,midg 3.4134581E-03 -8.8109579E-03 1,midg,midg; igrid,midg,midg 2.9531211E-02 1.7638592E-02 gauss-seidel spectral radius is 0.9984511 estimated iterations to convergence 202 setup time was (sec) 0.8200000 now iterating at: 14:59:34 rms-change max change #iterations 3.778568 161.4135 at 10iterations 1.680691 66.74577 at 20iterations 0.7496810 26.75189 at 30iterations 0.3349536 12.80096 at 40iterations 0.1494555 5.641032 at 50iterations 6.6228636E-02 2.424040 at 60iterations 2.9678836E-02 1.006120 at 70iterations 1.3216046E-02 0.4741840 at 80iterations 5.8742510E-03 0.1958141 at 90iterations 2.6265732E-03 9.9769592E-02 at 100iterations 1.1682602E-03 3.8947582E-02 at 110iterations 5.2279228E-04 1.7256737E-02 at 120iterations finished qdiffx linear iterations at : 14:59:41 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 5.2279228E-04 1.7256737E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:59:41 7.776u 0.205s 0:08.36 95.3% 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 Sat Oct 15 2011 at 14:59:41 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 has a net charge of 0.5140 !!! WARNING: MET 254 has a net charge of -0.2720 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: 2.668132 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 2.668132 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.256012 assigned positive charge : 399.4456 centred at (gu) : 90.44009 93.46376 78.84453 assigned negative charge : -394.1907 centred at (gu) : 90.48895 93.41739 78.38203 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25179 grid for indexing accessible points = 1.400000 m= 70406 mr = 106610 m= 23082 mr = 54664 m= 4815 mr = 17408 m= 558 mr = 3307 m= 28 mr = 313 m= 0 mr = 3 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 1.270000 number of dielectric boundary points 70175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 20402 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) : 1.778755 object centre at (A) : 1.108000 -3.728000 9.682002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6713569 0.6233854 midg,1,midg; midg,igrid,midg 2.1898046E-02 -8.8752314E-02 1,midg,midg; igrid,midg,midg 0.6217868 0.1587652 gauss-seidel spectral radius is 0.9992182 estimated iterations to convergence 282 setup time was (sec) 1.590000 now iterating at: 14:59:43 rms-change max change #iterations 9.257375 272.8151 at 10iterations 5.367449 144.9157 at 20iterations 3.077354 71.16084 at 30iterations 1.760593 42.78973 at 40iterations 1.005072 23.42695 at 50iterations 0.5698583 11.51003 at 60iterations 0.3233818 6.728558 at 70iterations 0.1833077 3.849098 at 80iterations 0.1038797 2.446493 at 90iterations 5.8685534E-02 1.176008 at 100iterations 3.3191256E-02 0.6488171 at 110iterations 1.8793467E-02 0.3494234 at 120iterations 1.0605287E-02 0.2095871 at 130iterations 5.9996992E-03 0.1181855 at 140iterations 3.3924491E-03 6.8086624E-02 at 150iterations 1.9193797E-03 3.6929131E-02 at 160iterations 1.0838392E-03 2.0002365E-02 at 170iterations 6.1222987E-04 1.2073040E-02 at 180iterations finished qdiffx linear iterations at : 14:59:54 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 6.1222987E-04 1.2073040E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 14:59:54 12.305u 0.225s 0:13.09 95.6% 0+0k 0+0io 0pf+0w