Mon Nov 29 15:03:54 PST 2010 #!/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 Nov 29 2010 at 15:03:54 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 0.4994389 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 0.4994389 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 91.30943 94.90833 89.22078 assigned negative charge : -408.5823 centred at (gu) : 91.26785 94.98487 89.87395 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4860 nv = 96 ne = 84 npr = 57715 no. pairs analyzed = 57715 no. exposed pairs = 3966 no. arc points = 28456 no. surface atoms = 1349 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 = 1.680000 m= 155 mr = 2213 m= 1 mr = 2 m= 0 mr = 0 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 2801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2639 ## 356 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4459516E-10 -4.4266119E-10 midg,1,midg; midg,igrid,midg 4.0604669E-11 2.3541613E-11 1,midg,midg; igrid,midg,midg 3.0094389E-11 1.6244008E-10 gauss-seidel spectral radius is 0.9793887 estimated iterations to convergence 58 setup time was (sec) 0.4000000 now iterating at: 15:03:55 rms-change max change #iterations 4.3019231E-02 10.22620 at 10iterations 2.3215045E-03 0.3867950 at 20iterations 1.3446317E-04 2.4444580E-02 at 30iterations 1.0445845E-05 1.9378662E-03 at 40iterations 1.1532201E-06 2.3138523E-04 at 50iterations finished qdiffx linear iterations at : 15:03:58 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.1532201E-06 2.3138523E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 15:03:58 3.431u 0.188s 0:03.91 92.3% 0+0k 0+0io 6pf+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 Nov 29 2010 at 15:03:58 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 1.498317 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 1.498317 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 93.92752 104.7242 87.66168 assigned negative charge : -408.5823 centred at (gu) : 93.80348 104.9542 89.62164 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 54429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13576 mr = 34264 m= 1012 mr = 8341 m= 13 mr = 377 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 26048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 21114 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) : 0.4994389 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9503790E-02 -2.7291559E-02 midg,1,midg; midg,igrid,midg 1.9157300E-03 4.9121026E-03 1,midg,midg; igrid,midg,midg -5.3832209E-04 1.6285741E-03 gauss-seidel spectral radius is 0.9978007 estimated iterations to convergence 170 setup time was (sec) 0.4800000 now iterating at: 15:03:59 rms-change max change #iterations 2.570278 161.5478 at 10iterations 0.9701107 44.72781 at 20iterations 0.3683329 16.76560 at 30iterations 0.1406902 5.730127 at 40iterations 5.3531196E-02 2.074913 at 50iterations 2.0347923E-02 0.8979174 at 60iterations 7.8073256E-03 0.3214378 at 70iterations 2.9739689E-03 0.1205225 at 80iterations 1.1324311E-03 4.7904968E-02 at 90iterations 4.3426757E-04 1.6288757E-02 at 100iterations 1.6540424E-04 7.1728230E-03 at 110iterations 6.2986335E-05 2.5305748E-03 at 120iterations finished qdiffx linear iterations at : 15:04:06 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 6.2986335E-05 2.5305748E-03 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 15:04:06 7.647u 0.219s 0:08.13 96.5% 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 Mon Nov 29 2010 at 15:04:06 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 2.247475 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 2.247475 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 95.89114 112.0861 86.49230 assigned negative charge : -408.5823 centred at (gu) : 95.70511 112.4313 89.43230 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 126801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 49771 mr = 85274 m= 11467 mr = 36886 m= 1315 mr = 7813 m= 59 mr = 750 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 58681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22533 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) : 1.498317 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.084687 -0.4901397 midg,1,midg; midg,igrid,midg 2.5496682E-02 1.8313538E-02 1,midg,midg; igrid,midg,midg -4.2415252E-03 1.3197823E-02 gauss-seidel spectral radius is 0.9989762 estimated iterations to convergence 247 setup time was (sec) 0.8800000 now iterating at: 15:04:07 rms-change max change #iterations 6.967410 209.8820 at 10iterations 3.685093 98.00730 at 20iterations 1.929581 47.03084 at 30iterations 1.007321 24.10126 at 40iterations 0.5243322 13.58155 at 50iterations 0.2736729 7.251032 at 60iterations 0.1421138 3.668785 at 70iterations 7.4153997E-02 1.852230 at 80iterations 3.8471844E-02 0.8912010 at 90iterations 2.0012738E-02 0.4447651 at 100iterations 1.0390732E-02 0.2366138 at 110iterations 5.3954655E-03 0.1241007 at 120iterations 2.8053366E-03 6.4620972E-02 at 130iterations 1.4573797E-03 3.3226013E-02 at 140iterations 7.5666024E-04 1.6429901E-02 at 150iterations 3.9324749E-04 9.2535019E-03 at 160iterations 2.0426480E-04 4.7068596E-03 at 170iterations 1.0625134E-04 2.7046204E-03 at 180iterations finished qdiffx linear iterations at : 15:04:18 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 1.0625134E-04 2.7046204E-03 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 15:04:19 12.150u 0.243s 0:12.66 97.8% 0+0k 0+0io 0pf+0w