Mon Oct 10 16:57:51 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 16:57:51 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 = 2845 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5523404 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): -36.24900 19.99500 ymin,ymax (A): -14.66100 30.07500 zmin,zma (A): 9.388000 73.84100 x,y,z range (A): 56.24400 44.73600 64.45300 scale (grids/A): 0.5523404 object centre (A): -8.127001 7.707000 41.61450 number of atom coordinates read : 2845 total number of charged atoms : 2705 net assigned charge : 1.500021 assigned positive charge : 422.7126 centred at (gu) : 90.50136 90.63010 90.26016 assigned negative charge : -421.2134 centred at (gu) : 90.52254 90.49446 90.26543 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 57245 no. pairs analyzed = 57245 no. exposed pairs = 3627 no. arc points = 25631 no. surface atoms = 1234 nbur = 1611 mkacc time = 0.1000000 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 = 1.540000 m= 227 mr = 2874 m= 0 mr = 5 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2570 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7324 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4622509E-10 7.6041340E-11 midg,1,midg; midg,igrid,midg -8.4194940E-10 1.3760320E-09 1,midg,midg; igrid,midg,midg 2.4960412E-10 -6.3827839E-11 gauss-seidel spectral radius is 0.9830865 estimated iterations to convergence 63 setup time was (sec) 0.3900000 now iterating at: 16:57:51 rms-change max change #iterations 7.5486138E-02 12.01136 at 10iterations 5.1845796E-03 0.8040581 at 20iterations 3.6207712E-04 6.2876999E-02 at 30iterations 2.7415113E-05 5.0013065E-03 at 40iterations 3.3685365E-06 8.3112717E-04 at 50iterations finished qdiffx linear iterations at : 16:57:54 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.3685365E-06 8.3112717E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 16:57:55 3.512u 0.187s 0:04.46 82.7% 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 16:57:55 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 = 2845 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: 1.657021 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): -36.24900 19.99500 ymin,ymax (A): -14.66100 30.07500 zmin,zma (A): 9.388000 73.84100 x,y,z range (A): 56.24400 44.73600 64.45300 scale (grids/A): 1.657021 object centre (A): -8.127001 7.707000 41.61450 number of atom coordinates read : 2845 total number of charged atoms : 2705 net assigned charge : 1.500021 assigned positive charge : 422.7126 centred at (gu) : 91.50348 91.88982 90.77969 assigned negative charge : -421.2134 centred at (gu) : 91.56723 91.48317 90.79604 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19119 mr = 41483 m= 2118 mr = 13193 m= 49 mr = 1064 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 715 time to turn everything in is 0.3200000 number of dielectric boundary points 27414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20790 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) : 0.5523404 object centre at (A) : -8.127001 7.707000 41.61450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6508207E-03 -1.3420616E-03 midg,1,midg; midg,igrid,midg -2.9595469E-03 8.2666194E-03 1,midg,midg; igrid,midg,midg 5.8471402E-03 -4.8700324E-03 gauss-seidel spectral radius is 0.9982278 estimated iterations to convergence 189 setup time was (sec) 0.5300000 now iterating at: 16:57:56 rms-change max change #iterations 3.320354 175.3957 at 10iterations 1.391100 52.78188 at 20iterations 0.5865096 21.25791 at 30iterations 0.2464050 9.203142 at 40iterations 0.1039100 3.878655 at 50iterations 4.3777999E-02 1.762894 at 60iterations 1.8384308E-02 0.6714935 at 70iterations 7.7620354E-03 0.2877903 at 80iterations 3.2534448E-03 0.1146011 at 90iterations 1.3845181E-03 5.1979065E-02 at 100iterations 5.8079133E-04 2.1753311E-02 at 110iterations 2.4434036E-04 8.5811615E-03 at 120iterations finished qdiffx linear iterations at : 16:58:04 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.4434036E-04 8.5811615E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 16:58:04 7.985u 0.208s 0:08.70 94.0% 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 Mon Oct 10 2011 at 16:58:04 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 = 2845 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: 2.485532 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): -36.24900 19.99500 ymin,ymax (A): -14.66100 30.07500 zmin,zma (A): 9.388000 73.84100 x,y,z range (A): 56.24400 44.73600 64.45300 scale (grids/A): 2.485532 object centre (A): -8.127001 7.707000 41.61450 number of atom coordinates read : 2845 total number of charged atoms : 2705 net assigned charge : 1.500021 assigned positive charge : 422.7126 centred at (gu) : 92.25510 92.83456 91.16946 assigned negative charge : -421.2134 centred at (gu) : 92.35091 92.22481 91.19403 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 143702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25631 grid for indexing accessible points = 1.400000 m= 65585 mr = 101610 m= 19109 mr = 51861 m= 3310 mr = 14288 m= 232 mr = 2254 m= 4 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2279 time to turn everything in is 0.7500000 number of dielectric boundary points 61814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21614 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) : 1.657021 object centre at (A) : -8.127001 7.707000 41.61450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1355759 -2.6905376E-02 midg,1,midg; midg,igrid,midg -5.8482148E-02 8.0616213E-02 1,midg,midg; igrid,midg,midg 6.9197133E-02 4.1628992E-03 gauss-seidel spectral radius is 0.9991487 estimated iterations to convergence 271 setup time was (sec) 0.9800000 now iterating at: 16:58:05 rms-change max change #iterations 8.468975 260.7910 at 10iterations 4.719142 128.9490 at 20iterations 2.627050 58.77738 at 30iterations 1.460999 32.33310 at 40iterations 0.8090753 18.77039 at 50iterations 0.4468066 9.803726 at 60iterations 0.2473937 5.613361 at 70iterations 0.1365954 2.952297 at 80iterations 7.5179294E-02 1.704563 at 90iterations 4.1604545E-02 1.003952 at 100iterations 2.2969112E-02 0.4809875 at 110iterations 1.2631971E-02 0.2826004 at 120iterations 6.9673825E-03 0.1475601 at 130iterations 3.8397727E-03 7.8125477E-02 at 140iterations 2.1219596E-03 4.3571472E-02 at 150iterations 1.1766787E-03 2.4566650E-02 at 160iterations 6.5300334E-04 1.4536858E-02 at 170iterations 3.6521343E-04 7.8582764E-03 at 180iterations finished qdiffx linear iterations at : 16:58:17 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 3.6521343E-04 7.8582764E-03 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 16:58:17 12.552u 0.241s 0:13.30 96.1% 0+0k 0+0io 0pf+0w