Tue Oct 11 06:03:30 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 Tue Oct 11 2011 at 06:03:30 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 0.7314718 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 0.7314718 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.13249 90.50535 90.29001 assigned negative charge : -311.0742 centred at (gu) : 89.26923 90.44883 90.37379 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7665 nv = 96 ne = 84 npr = 41821 no. pairs analyzed = 41821 no. exposed pairs = 2559 no. arc points = 17416 no. surface atoms = 876 nbur = 1405 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 553 mr = 4483 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1547 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8207 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5418431E-07 2.5087440E-08 midg,1,midg; midg,igrid,midg 4.3073101E-08 1.5437861E-07 1,midg,midg; igrid,midg,midg 2.4239546E-07 -1.6698179E-08 gauss-seidel spectral radius is 0.9902529 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 06:03:31 rms-change max change #iterations 0.2251605 29.71562 at 10iterations 2.9990697E-02 4.249664 at 20iterations 4.2898813E-03 0.5324993 at 30iterations 7.4274547E-04 8.3541870E-02 at 40iterations 2.0060816E-04 2.4007797E-02 at 50iterations finished qdiffx linear iterations at : 06:03:34 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.0060816E-04 2.4007797E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:03:35 3.298u 0.182s 0:04.19 82.8% 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 Tue Oct 11 2011 at 06:03:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 2.194415 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 2.194415 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 87.39761 91.51624 90.87011 assigned negative charge : -311.0742 centred at (gu) : 87.80787 91.34662 91.12144 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 80838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17416 grid for indexing accessible points = 1.400000 m= 34217 mr = 58004 m= 7367 mr = 26404 m= 765 mr = 5137 m= 24 mr = 467 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15584 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) : 0.7314718 object centre at (A) : 48.83300 5.693501 25.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5789190E-02 3.2321930E-02 midg,1,midg; midg,igrid,midg 5.0793651E-02 3.4706160E-02 1,midg,midg; igrid,midg,midg 5.1305104E-02 -5.8211632E-02 gauss-seidel spectral radius is 0.9988975 estimated iterations to convergence 238 setup time was (sec) 0.9000000 now iterating at: 06:03:36 rms-change max change #iterations 4.864322 182.8846 at 10iterations 2.454575 82.69344 at 20iterations 1.243548 35.60990 at 30iterations 0.6295643 19.57821 at 40iterations 0.3185796 9.880562 at 50iterations 0.1621430 4.475403 at 60iterations 8.2174271E-02 2.339785 at 70iterations 4.1706886E-02 1.123032 at 80iterations 2.1243975E-02 0.6924438 at 90iterations 1.0889106E-02 0.3444786 at 100iterations 5.5861589E-03 0.1722908 at 110iterations 2.9313869E-03 8.2237244E-02 at 120iterations finished qdiffx linear iterations at : 06:03:43 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.9313869E-03 8.2237244E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 06:03:43 7.847u 0.222s 0:08.39 96.0% 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 Tue Oct 11 2011 at 06:03:43 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 3.291623 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 3.291623 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 86.09630 92.27434 91.30512 assigned negative charge : -311.0742 centred at (gu) : 86.71181 92.01991 91.68213 start vw surface at 0.1300000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 186183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17416 grid for indexing accessible points = 1.400000 m= 104340 mr = 139132 m= 45085 mr = 87725 m= 13933 mr = 37498 m= 3153 mr = 11160 m= 446 mr = 2407 m= 30 mr = 339 m= 0 mr = 13 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 74896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15688 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) : 2.194415 object centre at (A) : 48.83300 5.693501 25.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1224779 0.2809687 midg,1,midg; midg,igrid,midg 0.3806207 0.1949468 1,midg,midg; igrid,midg,midg 0.4779027 -0.6849778 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.250000 now iterating at: 06:03:45 rms-change max change #iterations 10.63704 307.2883 at 10iterations 6.335539 123.6433 at 20iterations 3.772563 68.07063 at 30iterations 2.247694 41.51221 at 40iterations 1.332571 24.53189 at 50iterations 0.7876874 13.87522 at 60iterations 0.4661380 8.319419 at 70iterations 0.2750758 4.968408 at 80iterations 0.1627638 2.760256 at 90iterations 9.5961280E-02 1.992961 at 100iterations 5.6641754E-02 1.012999 at 110iterations 3.3649288E-02 0.6010666 at 120iterations 2.0006130E-02 0.3783913 at 130iterations 1.2059345E-02 0.2174835 at 140iterations 7.3990021E-03 0.1291599 at 150iterations 4.6877917E-03 8.5262299E-02 at 160iterations 3.1212245E-03 5.3960085E-02 at 170iterations 2.2141514E-03 3.8524628E-02 at 180iterations finished qdiffx linear iterations at : 06:03:56 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 2.2141514E-03 3.8524628E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 06:03:57 12.891u 0.200s 0:13.45 97.3% 0+0k 0+0io 0pf+0w