Sat Oct 8 11:37:19 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 8 2011 at 11:37:19 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4410 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 0.5847665 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): -25.55300 35.32600 ymin,ymax (A): 34.90800 94.97900 zmin,zma (A): 31.05100 88.11400 x,y,z range (A): 60.87900 60.07100 57.06300 scale (grids/A): 0.5847665 object centre (A): 4.886500 64.94350 59.58250 number of atom coordinates read : 4410 total number of charged atoms : 4262 net assigned charge : -1.985943 assigned positive charge : 666.2123 centred at (gu) : 90.98504 89.32467 89.04105 assigned negative charge : -668.2012 centred at (gu) : 90.82336 89.47020 89.20624 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9580 nv = 96 ne = 84 npr = 94353 no. pairs analyzed = 94353 no. exposed pairs = 4859 no. arc points = 32733 no. surface atoms = 1654 nbur = 2756 mkacc time = 0.2500000 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= 381 mr = 5653 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 139 time to turn everything in is 0.4900000 number of dielectric boundary points 4279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3440 ## 384 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 12563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0274511E-09 -5.7402314E-09 midg,1,midg; midg,igrid,midg 5.7049352E-09 -5.4613740E-09 1,midg,midg; igrid,midg,midg -5.5933702E-09 6.9062662E-09 gauss-seidel spectral radius is 0.9850025 estimated iterations to convergence 67 setup time was (sec) 0.8500000 now iterating at: 11:37:21 rms-change max change #iterations 0.1283830 15.12024 at 10iterations 1.0498870E-02 1.430996 at 20iterations 1.0932157E-03 0.1665630 at 30iterations 2.5697565E-04 3.7446976E-02 at 40iterations 9.1924820E-05 1.3736725E-02 at 50iterations finished qdiffx linear iterations at : 11:37:25 total time elapsed so far: 5.300000 # loops : 50 mean,max change (kT/e) : 9.1924820E-05 1.3736725E-02 energy calculations done at 5.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.470000 DelPhi exited at 11:37:26 5.471u 0.440s 0:06.39 92.4% 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 11:37:26 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4410 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 1.754300 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): -25.55300 35.32600 ymin,ymax (A): 34.90800 94.97900 zmin,zma (A): 31.05100 88.11400 x,y,z range (A): 60.87900 60.07100 57.06300 scale (grids/A): 1.754300 object centre (A): 4.886500 64.94350 59.58250 number of atom coordinates read : 4410 total number of charged atoms : 4262 net assigned charge : -1.985943 assigned positive charge : 666.2123 centred at (gu) : 92.95372 87.97276 87.12203 assigned negative charge : -668.2012 centred at (gu) : 92.46939 88.41036 87.61819 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 105486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32733 grid for indexing accessible points = 1.400000 m= 36418 mr = 76827 m= 4554 mr = 27492 m= 154 mr = 2660 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 8434 time to turn everything in is 0.8700000 number of dielectric boundary points 39605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 33076 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) : 0.5847665 object centre at (A) : 4.886500 64.94350 59.58250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4646509E-02 -4.0547706E-02 midg,1,midg; midg,igrid,midg 2.6083980E-02 -2.1275664E-02 1,midg,midg; igrid,midg,midg -2.2616968E-02 4.5314115E-02 gauss-seidel spectral radius is 0.9985502 estimated iterations to convergence 208 setup time was (sec) 1.240000 now iterating at: 11:37:28 rms-change max change #iterations 4.939612 159.2389 at 10iterations 2.251975 64.99205 at 20iterations 1.030158 30.99590 at 30iterations 0.4725084 13.06477 at 40iterations 0.2162884 5.591614 at 50iterations 9.9534482E-02 2.961163 at 60iterations 4.5640934E-02 1.270847 at 70iterations 2.0935606E-02 0.5511637 at 80iterations 9.6781850E-03 0.2797775 at 90iterations 4.4602551E-03 0.1340138 at 100iterations 2.0832832E-03 5.8255196E-02 at 110iterations 9.9604053E-04 3.0266762E-02 at 120iterations finished qdiffx linear iterations at : 11:37:40 total time elapsed so far: 13.79000 # loops : 120 mean,max change (kT/e) : 9.9604053E-04 3.0266762E-02 energy calculations done at 13.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.98000 DelPhi exited at 11:37:41 13.980u 0.515s 0:14.82 97.7% 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 Sat Oct 8 2011 at 11:37:41 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4410 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 2.631449 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): -25.55300 35.32600 ymin,ymax (A): 34.90800 94.97900 zmin,zma (A): 31.05100 88.11400 x,y,z range (A): 60.87900 60.07100 57.06300 scale (grids/A): 2.631449 object centre (A): 4.886500 64.94350 59.58250 number of atom coordinates read : 4410 total number of charged atoms : 4262 net assigned charge : -1.985943 assigned positive charge : 666.2123 centred at (gu) : 94.43014 86.95880 85.68270 assigned negative charge : -668.2012 centred at (gu) : 93.70403 87.61533 86.42705 start vw surface at 0.1600000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 244881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32733 grid for indexing accessible points = 1.400000 m= 123206 mr = 186046 m= 39663 mr = 102562 m= 7731 mr = 32032 m= 737 mr = 5629 m= 21 mr = 429 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 28340 time to turn everything in is 2.240000 number of dielectric boundary points 89541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 34089 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) : 1.754300 object centre at (A) : 4.886500 64.94350 59.58250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6961859 -0.5099451 midg,1,midg; midg,igrid,midg 0.3418117 -0.4602621 1,midg,midg; igrid,midg,midg -0.2704532 0.5169024 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 2.660000 now iterating at: 11:37:44 rms-change max change #iterations 11.83856 341.9600 at 10iterations 6.944338 136.3715 at 20iterations 4.031124 93.85776 at 30iterations 2.345032 41.02055 at 40iterations 1.357458 21.24331 at 50iterations 0.7854967 12.85260 at 60iterations 0.4528853 7.587452 at 70iterations 0.2612462 4.156497 at 80iterations 0.1507440 2.637820 at 90iterations 8.6910442E-02 1.436028 at 100iterations 5.0107099E-02 0.9066505 at 110iterations 2.8833291E-02 0.4529660 at 120iterations 1.6649934E-02 0.2583714 at 130iterations 9.6122958E-03 0.1522751 at 140iterations 5.5623818E-03 8.7833405E-02 at 150iterations 3.2392179E-03 5.1527888E-02 at 160iterations 1.9056004E-03 3.2107353E-02 at 170iterations 1.1402563E-03 2.0074129E-02 at 180iterations finished qdiffx linear iterations at : 11:38:04 total time elapsed so far: 22.63000 # loops : 180 mean,max change (kT/e) : 1.1402563E-03 2.0074129E-02 energy calculations done at 22.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.79000 DelPhi exited at 11:38:04 22.798u 0.550s 0:23.69 98.5% 0+0k 0+0io 0pf+0w