Mon Oct 10 13:58:14 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 Mon Oct 10 2011 at 13:58:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 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: 0.6480976 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): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 0.6480976 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 89.07823 90.87878 88.91183 assigned negative charge : -329.4240 centred at (gu) : 89.33768 90.96136 88.96436 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 44072 no. pairs analyzed = 44072 no. exposed pairs = 2782 no. arc points = 19526 no. surface atoms = 935 nbur = 1213 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3150 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3000000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1929 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1875555E-09 -1.5596418E-08 midg,1,midg; midg,igrid,midg -2.5834395E-09 -2.8011870E-08 1,midg,midg; igrid,midg,midg 2.2089257E-08 -3.7704257E-08 gauss-seidel spectral radius is 0.9876227 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 13:58:15 rms-change max change #iterations 0.1407455 21.68308 at 10iterations 1.4318330E-02 2.187796 at 20iterations 1.4395025E-03 0.2235603 at 30iterations 1.4268709E-04 2.4415970E-02 at 40iterations 1.4792413E-05 2.4871826E-03 at 50iterations finished qdiffx linear iterations at : 13:58:18 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.4792413E-05 2.4871826E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 13:58:19 3.536u 0.120s 0:04.16 87.7% 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 Mon Oct 10 2011 at 13:58:19 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 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: 1.944293 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): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 1.944293 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 87.23449 92.63641 86.73534 assigned negative charge : -329.4240 centred at (gu) : 88.01319 92.88409 86.89292 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 64057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19526 grid for indexing accessible points = 1.400000 m= 22637 mr = 43236 m= 3451 mr = 16324 m= 174 mr = 2037 m= 4 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.5500000 number of dielectric boundary points 28687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15812 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) : 0.6480976 object centre at (A) : 12.01100 -1.604000 14.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6928682E-03 -1.7723396E-02 midg,1,midg; midg,igrid,midg -3.7707279E-03 -1.5655909E-02 1,midg,midg; igrid,midg,midg 2.9353471E-02 -7.3033564E-02 gauss-seidel spectral radius is 0.9986409 estimated iterations to convergence 215 setup time was (sec) 0.8500000 now iterating at: 13:58:20 rms-change max change #iterations 4.003751 235.5309 at 10iterations 1.875544 67.70998 at 20iterations 0.8783975 31.49710 at 30iterations 0.4101540 13.50370 at 40iterations 0.1939630 6.950366 at 50iterations 9.0700828E-02 3.075912 at 60iterations 4.2528372E-02 1.358564 at 70iterations 1.9955019E-02 0.6204033 at 80iterations 9.3402378E-03 0.3205414 at 90iterations 4.3703779E-03 0.1485286 at 100iterations 2.0537488E-03 6.7144394E-02 at 110iterations 9.5993711E-04 3.5392761E-02 at 120iterations finished qdiffx linear iterations at : 13:58:26 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 9.5993711E-04 3.5392761E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 13:58:27 7.567u 0.202s 0:08.17 94.9% 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 Mon Oct 10 2011 at 13:58:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 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: 2.916439 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): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 2.916439 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 322.4239 centred at (gu) : 85.85178 93.95464 85.10309 assigned negative charge : -329.4240 centred at (gu) : 87.01982 94.32616 85.33936 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19526 grid for indexing accessible points = 1.400000 m= 73046 mr = 104988 m= 26256 mr = 58934 m= 6051 mr = 20814 m= 738 mr = 4352 m= 27 mr = 421 m= 0 mr = 6 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 1.280000 number of dielectric boundary points 64603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 16055 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) : 1.944293 object centre at (A) : 12.01100 -1.604000 14.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2309742E-02 -0.1772467 midg,1,midg; midg,igrid,midg -7.9224601E-02 -8.7345988E-02 1,midg,midg; igrid,midg,midg 0.3214777 -0.7346228 gauss-seidel spectral radius is 0.9992508 estimated iterations to convergence 288 setup time was (sec) 1.570000 now iterating at: 13:58:29 rms-change max change #iterations 9.370166 344.5216 at 10iterations 5.415744 128.9503 at 20iterations 3.135577 63.29617 at 30iterations 1.803220 37.55061 at 40iterations 1.036882 20.73721 at 50iterations 0.5944244 13.03428 at 60iterations 0.3413762 6.770782 at 70iterations 0.1955026 4.041740 at 80iterations 0.1120516 2.314133 at 90iterations 6.4260624E-02 1.308978 at 100iterations 3.6727984E-02 0.6894379 at 110iterations 2.1024011E-02 0.3905849 at 120iterations 1.2037563E-02 0.2266178 at 130iterations 6.8774074E-03 0.1391907 at 140iterations 3.9406926E-03 7.4815750E-02 at 150iterations 2.2517832E-03 4.2271137E-02 at 160iterations 1.2877908E-03 2.6947021E-02 at 170iterations 7.3779305E-04 1.4019012E-02 at 180iterations finished qdiffx linear iterations at : 13:58:39 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 7.3779305E-04 1.4019012E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 13:58:40 11.921u 0.195s 0:12.57 96.3% 0+0k 0+0io 0pf+0w