Sat Oct 8 16:11:12 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 16:11:12 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 = 2397 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: 0.6555083 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 0.6555083 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2337 net assigned charge : 4.000004 assigned positive charge : 359.7028 centred at (gu) : 90.78175 89.11135 90.39391 assigned negative charge : -355.7036 centred at (gu) : 90.83744 89.21815 90.43954 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7061 nv = 96 ne = 84 npr = 47688 no. pairs analyzed = 47688 no. exposed pairs = 2985 no. arc points = 20665 no. surface atoms = 1017 nbur = 1380 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3986 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2900000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2015 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8431 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4993230E-08 1.6313709E-09 midg,1,midg; midg,igrid,midg 3.1322507E-08 -6.9482193E-09 1,midg,midg; igrid,midg,midg 1.5204142E-08 -2.1720671E-10 gauss-seidel spectral radius is 0.9879228 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 16:11:12 rms-change max change #iterations 0.1541963 28.34109 at 10iterations 1.6204901E-02 2.412434 at 20iterations 1.7795010E-03 0.2964916 at 30iterations 2.1898722E-04 3.3041000E-02 at 40iterations 3.9200851E-05 6.6175461E-03 at 50iterations finished qdiffx linear iterations at : 16:11:15 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.9200851E-05 6.6175461E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 16:11:15 3.133u 0.134s 0:03.58 91.0% 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 8 2011 at 16:11:15 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 = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.966525 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 1.966525 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2337 net assigned charge : 4.000004 assigned positive charge : 359.7028 centred at (gu) : 92.34476 87.33329 91.18100 assigned negative charge : -355.7036 centred at (gu) : 92.51192 87.65445 91.31857 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 76360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 27985 mr = 53925 m= 4877 mr = 20828 m= 330 mr = 3309 m= 2 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 543 time to turn everything in is 0.5200000 number of dielectric boundary points 31352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18441 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) : 0.6555083 object centre at (A) : 22.24150 6.028500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5504022E-02 -1.3070283E-02 midg,1,midg; midg,igrid,midg 2.8861620E-02 -3.0850819E-03 1,midg,midg; igrid,midg,midg 1.3965113E-02 -4.2825356E-02 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 0.7800000 now iterating at: 16:11:16 rms-change max change #iterations 4.315979 190.5592 at 10iterations 2.052591 83.12716 at 20iterations 0.9773654 30.49768 at 30iterations 0.4676242 14.59844 at 40iterations 0.2235882 6.964314 at 50iterations 0.1069761 3.378594 at 60iterations 5.1110119E-02 1.659374 at 70iterations 2.4361916E-02 0.7654438 at 80iterations 1.1655047E-02 0.3727951 at 90iterations 5.5590891E-03 0.1750262 at 100iterations 2.6773761E-03 8.6906195E-02 at 110iterations 1.2835586E-03 3.9505005E-02 at 120iterations finished qdiffx linear iterations at : 16:11:22 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.2835586E-03 3.9505005E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 16:11:23 6.958u 0.184s 0:07.50 95.0% 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 8 2011 at 16:11:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 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: 2.949787 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 2.949787 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2337 net assigned charge : 4.000004 assigned positive charge : 359.7028 centred at (gu) : 93.51700 85.99986 91.77132 assigned negative charge : -355.7036 centred at (gu) : 93.76775 86.48166 91.97779 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 176548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 89549 mr = 130209 m= 33920 mr = 73745 m= 9130 mr = 27833 m= 1454 mr = 7080 m= 112 mr = 1049 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1784 time to turn everything in is 1.320000 number of dielectric boundary points 70736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 18695 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) : 1.966525 object centre at (A) : 22.24150 6.028500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1589535 -0.2520474 midg,1,midg; midg,igrid,midg 0.2233374 -6.2871620E-02 1,midg,midg; igrid,midg,midg 0.1257046 -0.6065350 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.600000 now iterating at: 16:11:25 rms-change max change #iterations 9.946600 420.0585 at 10iterations 5.845275 134.7540 at 20iterations 3.425636 65.40114 at 30iterations 2.009430 38.95319 at 40iterations 1.170602 24.21868 at 50iterations 0.6839989 14.63408 at 60iterations 0.3981817 8.541915 at 70iterations 0.2314692 4.099442 at 80iterations 0.1344844 2.433806 at 90iterations 7.7915348E-02 1.462408 at 100iterations 4.5240164E-02 0.7713553 at 110iterations 2.6254373E-02 0.4511738 at 120iterations 1.5219233E-02 0.3411980 at 130iterations 8.8274619E-03 0.1639071 at 140iterations 5.1175817E-03 9.5630646E-02 at 150iterations 2.9771184E-03 5.3037643E-02 at 160iterations 1.7377513E-03 3.3840179E-02 at 170iterations 1.0217960E-03 2.0236015E-02 at 180iterations finished qdiffx linear iterations at : 16:11:34 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 1.0217960E-03 2.0236015E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 16:11:35 11.391u 0.175s 0:11.86 97.4% 0+0k 0+0io 0pf+0w