Sun Oct 9 01:47:37 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 01:47:37 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 = 2341 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: 0.6434820 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 0.6434820 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.00002 assigned positive charge : 340.8824 centred at (gu) : 90.32640 88.70962 88.85575 assigned negative charge : -330.8831 centred at (gu) : 90.24883 88.84074 88.86141 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6590 nv = 96 ne = 84 npr = 47243 no. pairs analyzed = 47243 no. exposed pairs = 3088 no. arc points = 22161 no. surface atoms = 1032 nbur = 1309 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3395 m= 6 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2700000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2139 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0805876E-08 1.2029346E-08 midg,1,midg; midg,igrid,midg 3.9322231E-08 1.1711544E-09 1,midg,midg; igrid,midg,midg 6.8316495E-09 2.5899023E-08 gauss-seidel spectral radius is 0.9874701 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 01:47:38 rms-change max change #iterations 0.1352755 23.87691 at 10iterations 1.3500980E-02 1.935230 at 20iterations 1.4506816E-03 0.2100639 at 30iterations 2.1558680E-04 3.4715652E-02 at 40iterations 5.3987402E-05 1.0395050E-02 at 50iterations finished qdiffx linear iterations at : 01:47:40 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.3987402E-05 1.0395050E-02 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 01:47:41 3.357u 0.193s 0:03.82 92.6% 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 01:47:41 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 = 2341 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: 1.930446 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 1.930446 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.00002 assigned positive charge : 340.8824 centred at (gu) : 90.97900 86.12875 86.56696 assigned negative charge : -330.8831 centred at (gu) : 90.74626 86.52238 86.58421 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22161 grid for indexing accessible points = 1.400000 m= 25125 mr = 46368 m= 4240 mr = 17885 m= 297 mr = 2532 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 32478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17398 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) : 0.6434820 object centre at (A) : 26.38100 6.220000 56.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3316601E-02 3.7390772E-02 midg,1,midg; midg,igrid,midg 3.1677317E-02 -3.2602015E-03 1,midg,midg; igrid,midg,midg 1.1326184E-02 6.0899898E-02 gauss-seidel spectral radius is 0.9986488 estimated iterations to convergence 216 setup time was (sec) 0.8100000 now iterating at: 01:47:42 rms-change max change #iterations 3.979060 203.6035 at 10iterations 1.863309 72.53784 at 20iterations 0.8747231 30.43426 at 30iterations 0.4104676 15.70530 at 40iterations 0.1925604 6.333416 at 50iterations 9.0207092E-02 2.930706 at 60iterations 4.2410471E-02 1.472559 at 70iterations 1.9917654E-02 0.6763003 at 80iterations 9.3829660E-03 0.3425007 at 90iterations 4.4377176E-03 0.1467457 at 100iterations 2.1004891E-03 6.7474127E-02 at 110iterations 1.0040229E-03 3.6346436E-02 at 120iterations finished qdiffx linear iterations at : 01:47:51 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 1.0040229E-03 3.6346436E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 01:47:52 10.127u 0.305s 0:10.78 96.6% 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 01:47:52 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 = 2341 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: 2.895669 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): -1.281000 54.04300 ymin,ymax (A): -15.06700 27.50700 zmin,zma (A): 29.36500 83.62100 x,y,z range (A): 55.32400 42.57400 54.25600 scale (grids/A): 2.895669 object centre (A): 26.38100 6.220000 56.49300 number of atom coordinates read : 2341 total number of charged atoms : 2206 net assigned charge : 10.00002 assigned positive charge : 340.8824 centred at (gu) : 91.46835 84.19294 84.85040 assigned negative charge : -330.8831 centred at (gu) : 91.11945 84.78361 84.87642 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22161 grid for indexing accessible points = 1.400000 m= 79748 mr = 112940 m= 30130 mr = 63520 m= 7763 mr = 23677 m= 1264 mr = 5631 m= 102 mr = 808 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 73186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 17648 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) : 1.930446 object centre at (A) : 26.38100 6.220000 56.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3812262 0.4807166 midg,1,midg; midg,igrid,midg 0.2954960 -3.2960817E-02 1,midg,midg; igrid,midg,midg 3.2445751E-02 0.6230560 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 1.530000 now iterating at: 01:47:53 rms-change max change #iterations 9.507779 379.5339 at 10iterations 5.609095 141.6875 at 20iterations 3.292815 80.79560 at 30iterations 1.928082 41.45839 at 40iterations 1.123942 23.10834 at 50iterations 0.6542631 14.31485 at 60iterations 0.3792235 8.033012 at 70iterations 0.2202573 4.393328 at 80iterations 0.1274914 2.754517 at 90iterations 7.3830098E-02 1.499657 at 100iterations 4.2552367E-02 0.8011322 at 110iterations 2.4662144E-02 0.4966507 at 120iterations 1.4234671E-02 0.2587585 at 130iterations 8.2382197E-03 0.1597623 at 140iterations 4.7723805E-03 8.8175058E-02 at 150iterations 2.7735534E-03 5.4689884E-02 at 160iterations 1.6191315E-03 3.4091949E-02 at 170iterations 9.5472223E-04 2.0706177E-02 at 180iterations finished qdiffx linear iterations at : 01:48:04 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 9.5472223E-04 2.0706177E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 01:48:05 12.710u 0.210s 0:13.26 97.4% 0+0k 0+0io 0pf+0w