Tue Oct 11 03:26:43 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 03:26:43 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 = 2782 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: 0.5657259 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 0.5657259 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2635 net assigned charge : 8.000025 assigned positive charge : 426.8816 centred at (gu) : 87.83406 88.31143 89.67790 assigned negative charge : -418.8827 centred at (gu) : 87.77695 88.40091 89.72055 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5766 nv = 96 ne = 84 npr = 55320 no. pairs analyzed = 55320 no. exposed pairs = 3568 no. arc points = 24710 no. surface atoms = 1206 nbur = 1576 mkacc time = 9.0000004E-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 = 1.512000 m= 215 mr = 2993 m= 0 mr = 5 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2549 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6975983E-09 4.6033921E-10 midg,1,midg; midg,igrid,midg 3.2365570E-09 -5.8190661E-11 1,midg,midg; igrid,midg,midg 4.8097137E-10 1.0571823E-09 gauss-seidel spectral radius is 0.9838621 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 03:26:44 rms-change max change #iterations 8.3755061E-02 13.78030 at 10iterations 6.2971278E-03 1.021572 at 20iterations 9.4176835E-04 0.1827784 at 30iterations 4.0346425E-04 8.6677551E-02 at 40iterations 1.9558489E-04 4.2078972E-02 at 50iterations finished qdiffx linear iterations at : 03:26:48 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.9558489E-04 4.2078972E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 03:26:48 3.437u 0.195s 0:04.99 72.5% 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 03:26:48 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 = 2782 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: 1.697178 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 1.697178 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2635 net assigned charge : 8.000025 assigned positive charge : 426.8816 centred at (gu) : 83.50160 84.93353 89.03297 assigned negative charge : -418.8827 centred at (gu) : 83.33077 85.20278 89.16160 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24710 grid for indexing accessible points = 1.400000 m= 19321 mr = 43362 m= 1959 mr = 13181 m= 44 mr = 918 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.3100000 number of dielectric boundary points 27825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20330 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) : 0.5657259 object centre at (A) : 12.99950 6.530000 12.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8568918E-03 -7.1343820E-04 midg,1,midg; midg,igrid,midg 2.6320102E-02 -8.8025648E-03 1,midg,midg; igrid,midg,midg 3.4854303E-03 5.8022677E-05 gauss-seidel spectral radius is 0.9982970 estimated iterations to convergence 192 setup time was (sec) 0.5300000 now iterating at: 03:26:49 rms-change max change #iterations 3.456967 153.8604 at 10iterations 1.482104 58.10802 at 20iterations 0.6355322 26.41677 at 30iterations 0.2730507 9.993353 at 40iterations 0.1169992 4.948784 at 50iterations 5.0151419E-02 1.907063 at 60iterations 2.1563657E-02 0.7970853 at 70iterations 9.3416348E-03 0.3480339 at 80iterations 4.0883911E-03 0.1597419 at 90iterations 1.9162211E-03 8.3621979E-02 at 100iterations 1.0084795E-03 4.9271107E-02 at 110iterations 6.2740332E-04 2.7084351E-02 at 120iterations finished qdiffx linear iterations at : 03:26:56 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 6.2740332E-04 2.7084351E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:26:57 7.852u 0.200s 0:08.96 89.8% 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 03:26:57 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 = 2782 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: 2.545767 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 2.545767 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2635 net assigned charge : 8.000025 assigned positive charge : 426.8816 centred at (gu) : 80.25216 82.40041 88.54939 assigned negative charge : -418.8827 centred at (gu) : 79.99619 82.80408 88.74234 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 148862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24710 grid for indexing accessible points = 1.400000 m= 67593 mr = 106353 m= 18610 mr = 53236 m= 3034 mr = 13685 m= 224 mr = 2009 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 533 time to turn everything in is 0.7800000 number of dielectric boundary points 62931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21067 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) : 1.697178 object centre at (A) : 12.99950 6.530000 12.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8141346E-02 -6.5092952E-03 midg,1,midg; midg,igrid,midg 0.2922145 -0.1204116 1,midg,midg; igrid,midg,midg 6.7949168E-02 -5.3983368E-02 gauss-seidel spectral radius is 0.9991679 estimated iterations to convergence 274 setup time was (sec) 1.000000 now iterating at: 03:26:59 rms-change max change #iterations 8.797658 269.5510 at 10iterations 4.999996 149.0035 at 20iterations 2.835810 71.99414 at 30iterations 1.592520 40.38230 at 40iterations 0.8949842 20.36711 at 50iterations 0.5012998 12.37116 at 60iterations 0.2807897 5.893684 at 70iterations 0.1569370 3.483446 at 80iterations 8.7660193E-02 2.037699 at 90iterations 4.8919648E-02 1.062335 at 100iterations 2.7239477E-02 0.5795250 at 110iterations 1.5264380E-02 0.3440151 at 120iterations 8.5736113E-03 0.1742697 at 130iterations 4.8693945E-03 9.9786758E-02 at 140iterations 2.8326358E-03 6.5393448E-02 at 150iterations 1.7263915E-03 4.5608521E-02 at 160iterations 1.1396854E-03 2.8739929E-02 at 170iterations 8.2304026E-04 2.0946503E-02 at 180iterations finished qdiffx linear iterations at : 03:27:11 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 8.2304026E-04 2.0946503E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 03:27:11 12.510u 0.256s 0:14.07 90.6% 0+0k 0+0io 0pf+0w