Sun Oct 9 08:48:58 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 Sun Oct 9 2011 at 08:48:58 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 # of charge parameter records: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5265 !!! WARNING: HIR 698 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5174795 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 0.5174795 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.485990 assigned positive charge : 791.7563 centred at (gu) : 89.52486 89.80756 88.59498 assigned negative charge : -795.2485 centred at (gu) : 89.42190 89.89192 88.62731 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8899 nv = 96 ne = 84 npr = 107155 no. pairs analyzed = 107155 no. exposed pairs = 6613 no. arc points = 46108 no. surface atoms = 2214 nbur = 3051 mkacc time = 0.2400000 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 = 1.652000 m= 295 mr = 4576 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4514 ## 645 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11919 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4444979E-11 -1.3373375E-10 midg,1,midg; midg,igrid,midg 2.6780286E-10 -3.7633036E-10 1,midg,midg; igrid,midg,midg -5.3189930E-10 2.8578925E-10 gauss-seidel spectral radius is 0.9809350 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 08:48:59 rms-change max change #iterations 7.6494411E-02 12.73451 at 10iterations 4.4346498E-03 0.6021709 at 20iterations 3.3141262E-04 6.7083359E-02 at 30iterations 6.1763341E-05 1.6721725E-02 at 40iterations 1.7776398E-05 4.6672821E-03 at 50iterations finished qdiffx linear iterations at : 08:49:01 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.7776398E-05 4.6672821E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:49:02 3.358u 0.201s 0:03.88 91.4% 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 Sun Oct 9 2011 at 08:49:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5265 !!! WARNING: HIR 698 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.552438 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 1.552438 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.485990 assigned positive charge : 791.7563 centred at (gu) : 88.57283 89.42070 85.78301 assigned negative charge : -795.2485 centred at (gu) : 88.26535 89.67583 85.88140 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28055 mr = 68321 m= 2291 mr = 18157 m= 37 mr = 943 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1347 time to turn everything in is 0.6800000 number of dielectric boundary points 43046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 637 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 38457 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) : 0.5174795 object centre at (A) : 42.84650 1.312500 17.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0432103E-02 -1.6099589E-02 midg,1,midg; midg,igrid,midg 1.0964775E-02 -2.4673168E-03 1,midg,midg; igrid,midg,midg -1.9329164E-02 4.0927106E-03 gauss-seidel spectral radius is 0.9982170 estimated iterations to convergence 188 setup time was (sec) 0.9600000 now iterating at: 08:49:03 rms-change max change #iterations 4.130293 158.3331 at 10iterations 1.733133 63.55164 at 20iterations 0.7282522 23.93930 at 30iterations 0.3064775 9.840001 at 40iterations 0.1285855 4.568961 at 50iterations 5.4142069E-02 1.608335 at 60iterations 2.2817964E-02 0.6652490 at 70iterations 9.6232761E-03 0.2937632 at 80iterations 4.0647038E-03 0.1235619 at 90iterations 1.7123932E-03 5.5692673E-02 at 100iterations 7.3090114E-04 2.5842667E-02 at 110iterations 3.1508299E-04 1.2246132E-02 at 120iterations finished qdiffx linear iterations at : 08:49:10 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.1508299E-04 1.2246132E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:49:10 7.612u 0.263s 0:08.18 96.2% 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 Sun Oct 9 2011 at 08:49:10 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5265 !!! WARNING: HIR 698 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.328658 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 2.328658 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.485990 assigned positive charge : 791.7563 centred at (gu) : 87.85873 89.13048 83.67422 assigned negative charge : -795.2485 centred at (gu) : 87.39806 89.51372 83.82196 start vw surface at 0.2300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 233178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 101701 mr = 167973 m= 24453 mr = 78321 m= 3186 mr = 17353 m= 150 mr = 1892 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4575 time to turn everything in is 1.620000 number of dielectric boundary points 97092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 40718 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) : 1.552438 object centre at (A) : 42.84650 1.312500 17.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2998751 -0.3957934 midg,1,midg; midg,igrid,midg 0.1467515 -3.2240991E-02 1,midg,midg; igrid,midg,midg -0.4966491 2.5589613E-02 gauss-seidel spectral radius is 0.9992106 estimated iterations to convergence 281 setup time was (sec) 1.910000 now iterating at: 08:49:12 rms-change max change #iterations 11.10523 303.9203 at 10iterations 6.510746 161.9932 at 20iterations 3.776584 78.78898 at 30iterations 2.184783 44.26867 at 40iterations 1.258434 24.89781 at 50iterations 0.7217102 15.91174 at 60iterations 0.4136246 7.551781 at 70iterations 0.2359606 4.255144 at 80iterations 0.1347565 2.586426 at 90iterations 7.6908253E-02 1.321434 at 100iterations 4.3653890E-02 0.8399544 at 110iterations 2.4812950E-02 0.4817783 at 120iterations 1.4116330E-02 0.2465675 at 130iterations 8.0138175E-03 0.1382535 at 140iterations 4.5435005E-03 8.0844879E-02 at 150iterations 2.5801181E-03 4.3334961E-02 at 160iterations 1.4672189E-03 2.6570082E-02 at 170iterations 8.3588267E-04 1.4357567E-02 at 180iterations finished qdiffx linear iterations at : 08:49:22 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 8.3588267E-04 1.4357567E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 08:49:23 11.907u 0.225s 0:12.46 97.2% 0+0k 0+0io 0pf+0w