Sun Oct 9 16:21:52 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 Sun Oct 9 2011 at 16:21:52 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 = 3343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5943436 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 0.5943436 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3200 net assigned charge : 3.500013 assigned positive charge : 522.6873 centred at (gu) : 90.75986 88.57896 90.19695 assigned negative charge : -519.1887 centred at (gu) : 90.84734 88.66645 90.27782 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8008 nv = 96 ne = 84 npr = 63411 no. pairs analyzed = 63411 no. exposed pairs = 5040 no. arc points = 35533 no. surface atoms = 1670 nbur = 1673 mkacc time = 0.1300000 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 = 1.456000 m= 374 mr = 3573 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3520 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9890 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2968238E-09 -2.2057660E-09 midg,1,midg; midg,igrid,midg 6.6210921E-09 -1.6975347E-09 1,midg,midg; igrid,midg,midg 3.9998462E-09 -2.8564455E-09 gauss-seidel spectral radius is 0.9854351 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 16:21:53 rms-change max change #iterations 0.1196640 22.84606 at 10iterations 9.9806702E-03 1.365170 at 20iterations 1.0172141E-03 0.1427498 at 30iterations 1.8857532E-04 1.8432617E-02 at 40iterations 5.0752489E-05 3.6439896E-03 at 50iterations finished qdiffx linear iterations at : 16:21:55 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 5.0752489E-05 3.6439896E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 16:21:56 3.357u 0.152s 0:03.78 92.5% 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 Sun Oct 9 2011 at 16:21:56 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 = 3343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.783031 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 1.783031 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3200 net assigned charge : 3.500013 assigned positive charge : 522.6873 centred at (gu) : 92.27842 85.73560 90.59016 assigned negative charge : -519.1887 centred at (gu) : 92.54156 85.99899 90.83295 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35533 grid for indexing accessible points = 1.400000 m= 26112 mr = 53149 m= 3065 mr = 16239 m= 115 mr = 1339 m= 7 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 370 time to turn everything in is 0.6200000 number of dielectric boundary points 44540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 24950 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) : 0.5943436 object centre at (A) : -0.7500000 32.21550 319.0030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9010037E-02 -7.2651938E-02 midg,1,midg; midg,igrid,midg 2.3733176E-02 -2.0246373E-02 1,midg,midg; igrid,midg,midg 2.0011431E-02 1.6845422E-03 gauss-seidel spectral radius is 0.9985558 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 16:21:57 rms-change max change #iterations 4.438084 157.9060 at 10iterations 2.014966 68.34831 at 20iterations 0.9223515 32.19993 at 30iterations 0.4213853 14.30798 at 40iterations 0.1927857 6.430445 at 50iterations 8.7949134E-02 2.802534 at 60iterations 4.0249981E-02 1.216162 at 70iterations 1.8449895E-02 0.5578089 at 80iterations 8.4711015E-03 0.2642384 at 90iterations 3.8984823E-03 0.1234665 at 100iterations 1.7942191E-03 5.4153442E-02 at 110iterations 8.3139411E-04 2.6775360E-02 at 120iterations finished qdiffx linear iterations at : 16:22:03 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 8.3139411E-04 2.6775360E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 16:22:04 7.314u 0.191s 0:07.82 95.9% 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 16:22:04 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 = 3343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.674546 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 2.674546 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3200 net assigned charge : 3.500013 assigned positive charge : 522.6873 centred at (gu) : 93.41751 83.60310 90.88514 assigned negative charge : -519.1887 centred at (gu) : 93.81222 83.99839 91.24930 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 198963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35533 grid for indexing accessible points = 1.400000 m= 87733 mr = 131297 m= 25909 mr = 65045 m= 4743 mr = 17957 m= 456 mr = 2875 m= 24 mr = 185 m= 3 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1351 time to turn everything in is 1.430000 number of dielectric boundary points 100472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 25598 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) : 1.783031 object centre at (A) : -0.7500000 32.21550 319.0030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2979366 -1.199145 midg,1,midg; midg,igrid,midg 0.2756489 -0.3473517 1,midg,midg; igrid,midg,midg 0.2225556 -2.7776355E-02 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.750000 now iterating at: 16:22:06 rms-change max change #iterations 11.19063 359.6235 at 10iterations 6.838371 176.6592 at 20iterations 4.132502 92.89038 at 30iterations 2.476676 53.76431 at 40iterations 1.474211 33.07225 at 50iterations 0.8746021 16.62177 at 60iterations 0.5161456 10.33696 at 70iterations 0.3043827 6.273734 at 80iterations 0.1789178 3.475013 at 90iterations 0.1049853 1.993258 at 100iterations 6.1639454E-02 1.127567 at 110iterations 3.6040727E-02 0.7152405 at 120iterations 2.1072121E-02 0.3692522 at 130iterations 1.2302872E-02 0.2152853 at 140iterations 7.1899486E-03 0.1385102 at 150iterations 4.2046937E-03 8.4156036E-02 at 160iterations 2.4570732E-03 4.7761917E-02 at 170iterations 1.4367216E-03 2.3660660E-02 at 180iterations finished qdiffx linear iterations at : 16:22:16 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 1.4367216E-03 2.3660660E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 16:22:16 11.958u 0.199s 0:12.44 97.5% 0+0k 0+0io 0pf+0w