Sat Oct 15 10:23:17 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+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 10:23:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5822797 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 0.5822797 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 641.9063 centred at (gu) : 91.02283 88.83842 88.36399 assigned negative charge : -643.9094 centred at (gu) : 90.86806 88.99348 88.55753 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9350 nv = 96 ne = 84 npr = 88891 no. pairs analyzed = 88891 no. exposed pairs = 4908 no. arc points = 32850 no. surface atoms = 1680 nbur = 2580 mkacc time = 0.2000000 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= 393 mr = 5407 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.4200000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3519 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5555172E-09 -5.1001967E-09 midg,1,midg; midg,igrid,midg 5.9578085E-09 -4.6532009E-09 1,midg,midg; igrid,midg,midg -4.7985642E-09 5.7489262E-09 gauss-seidel spectral radius is 0.9848688 estimated iterations to convergence 67 setup time was (sec) 0.7100000 now iterating at: 10:23:18 rms-change max change #iterations 0.1227090 16.05250 at 10iterations 1.0598005E-02 1.453275 at 20iterations 1.7820286E-03 0.2605305 at 30iterations 5.7999167E-04 6.4643860E-02 at 40iterations 2.1694838E-04 2.1800995E-02 at 50iterations finished qdiffx linear iterations at : 10:23:22 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 2.1694838E-04 2.1800995E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 10:23:23 4.415u 0.245s 0:05.28 88.0% 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 10:23:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.746839 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 1.746839 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 641.9063 centred at (gu) : 93.06722 86.51411 85.09100 assigned negative charge : -643.9094 centred at (gu) : 92.60356 86.98039 85.67224 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 103805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32850 grid for indexing accessible points = 1.400000 m= 36115 mr = 75547 m= 4765 mr = 26655 m= 180 mr = 2832 m= 0 mr = 26 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3797 time to turn everything in is 0.7500000 number of dielectric boundary points 39805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 31939 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) : 0.5822797 object centre at (A) : 4.899499 65.59850 61.19800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8182269E-02 -3.2156859E-02 midg,1,midg; midg,igrid,midg 2.8991349E-02 -4.8764214E-02 1,midg,midg; igrid,midg,midg -1.4259908E-02 3.8991746E-02 gauss-seidel spectral radius is 0.9985318 estimated iterations to convergence 207 setup time was (sec) 1.090000 now iterating at: 10:23:24 rms-change max change #iterations 4.762535 175.5074 at 10iterations 2.163247 65.94611 at 20iterations 0.9851568 27.99261 at 30iterations 0.4502505 12.59438 at 40iterations 0.2058256 6.423161 at 50iterations 9.4104156E-02 2.566401 at 60iterations 4.3098938E-02 1.276916 at 70iterations 1.9840263E-02 0.5434265 at 80iterations 9.1905938E-03 0.2652302 at 90iterations 4.3435711E-03 0.1202030 at 100iterations 2.1278523E-03 6.4949036E-02 at 110iterations 1.1078528E-03 3.2657623E-02 at 120iterations finished qdiffx linear iterations at : 10:23:33 total time elapsed so far: 10.02000 # loops : 120 mean,max change (kT/e) : 1.1078528E-03 3.2657623E-02 energy calculations done at 10.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.20000 DelPhi exited at 10:23:34 10.202u 0.287s 0:11.12 94.2% 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 15 2011 at 10:23:34 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.620259 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): -25.67000 35.46900 ymin,ymax (A): 35.19500 96.00200 zmin,zma (A): 31.23500 91.16100 x,y,z range (A): 61.13900 60.80700 59.92599 scale (grids/A): 2.620259 object centre (A): 4.899499 65.59850 61.19800 number of atom coordinates read : 4260 total number of charged atoms : 4110 net assigned charge : -1.999959 assigned positive charge : 641.9063 centred at (gu) : 94.60045 84.77073 82.63618 assigned negative charge : -643.9094 centred at (gu) : 93.90533 85.47042 83.50822 start vw surface at 0.1800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 241270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32850 grid for indexing accessible points = 1.400000 m= 121202 mr = 183153 m= 39455 mr = 100017 m= 8125 mr = 31219 m= 830 mr = 5976 m= 23 mr = 503 m= 0 mr = 5 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 12520 time to turn everything in is 1.940000 number of dielectric boundary points 90032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 32870 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) : 1.746839 object centre at (A) : 4.899499 65.59850 61.19800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.009786 -0.3715747 midg,1,midg; midg,igrid,midg 0.3835178 -1.042657 1,midg,midg; igrid,midg,midg -8.2089499E-02 0.3018900 gauss-seidel spectral radius is 0.9992573 estimated iterations to convergence 290 setup time was (sec) 2.300000 now iterating at: 10:23:37 rms-change max change #iterations 11.59984 372.1346 at 10iterations 6.836388 140.5065 at 20iterations 3.979068 70.70723 at 30iterations 2.316746 38.35711 at 40iterations 1.342032 24.84725 at 50iterations 0.7763479 12.83415 at 60iterations 0.4489548 8.494372 at 70iterations 0.2584803 4.210155 at 80iterations 0.1494483 2.380049 at 90iterations 8.6008459E-02 1.466551 at 100iterations 4.9581785E-02 0.7970581 at 110iterations 2.8530946E-02 0.4369178 at 120iterations 1.6483175E-02 0.2622385 at 130iterations 9.5340088E-03 0.1423721 at 140iterations 5.5462732E-03 9.2630386E-02 at 150iterations 3.2627152E-03 5.6587219E-02 at 160iterations 1.9538526E-03 3.3424377E-02 at 170iterations 1.2059378E-03 1.9668579E-02 at 180iterations finished qdiffx linear iterations at : 10:23:51 total time elapsed so far: 16.82000 # loops : 180 mean,max change (kT/e) : 1.2059378E-03 1.9668579E-02 energy calculations done at 16.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.00000 DelPhi exited at 10:23:52 17.005u 0.324s 0:17.90 96.7% 0+0k 0+0io 0pf+0w