Sun Oct 9 20:43:33 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 20:43:33 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5695453 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 0.5695453 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4928 net assigned charge : 3.121028 assigned positive charge : 780.3818 centred at (gu) : 88.36873 88.90913 89.48120 assigned negative charge : -777.2664 centred at (gu) : 88.26408 88.88724 89.44379 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10654 nv = 96 ne = 84 npr = 103799 no. pairs analyzed = 103799 no. exposed pairs = 5966 no. arc points = 39513 no. surface atoms = 2045 nbur = 3037 mkacc time = 0.2700000 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 = 1.512000 m= 542 mr = 6104 m= 0 mr = 43 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 5049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4112 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4380916E-10 1.3581272E-09 midg,1,midg; midg,igrid,midg -8.0915295E-11 8.6746066E-10 1,midg,midg; igrid,midg,midg -3.4693510E-09 2.2475917E-09 gauss-seidel spectral radius is 0.9842476 estimated iterations to convergence 65 setup time was (sec) 0.8100000 now iterating at: 20:43:35 rms-change max change #iterations 0.1246518 19.53598 at 10iterations 1.2981026E-02 1.968582 at 20iterations 4.1124783E-03 0.4302902 at 30iterations 1.9981454E-03 0.2058449 at 40iterations 1.0063600E-03 0.1094373 at 50iterations finished qdiffx linear iterations at : 20:43:38 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.0063600E-03 0.1094373 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.820000 DelPhi exited at 20:43:39 4.829u 0.380s 0:05.53 94.0% 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 Sun Oct 9 2011 at 20:43:39 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.708636 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 1.708636 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4928 net assigned charge : 3.121028 assigned positive charge : 780.3818 centred at (gu) : 85.10482 86.72572 88.44281 assigned negative charge : -777.2664 centred at (gu) : 84.79211 86.66183 88.33105 start vw surface at 0.1700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39513 grid for indexing accessible points = 1.400000 m= 42536 mr = 85923 m= 5613 mr = 30996 m= 207 mr = 3201 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 46573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 38079 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) : 0.5695453 object centre at (A) : 33.12500 23.44850 29.41400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9709969E-02 -2.3439312E-03 midg,1,midg; midg,igrid,midg 2.1596948E-02 1.4735701E-02 1,midg,midg; igrid,midg,midg 2.9684477E-03 4.9745053E-02 gauss-seidel spectral radius is 0.9985325 estimated iterations to convergence 207 setup time was (sec) 1.270000 now iterating at: 20:43:41 rms-change max change #iterations 5.139243 199.0610 at 10iterations 2.331144 65.88961 at 20iterations 1.064171 27.83820 at 30iterations 0.4861831 13.97650 at 40iterations 0.2223408 6.119786 at 50iterations 0.1024152 2.995306 at 60iterations 4.7346491E-02 1.233604 at 70iterations 2.2460185E-02 0.5973282 at 80iterations 1.1300454E-02 0.3117828 at 90iterations 6.3260724E-03 0.1718705 at 100iterations 4.0214271E-03 0.1077843 at 110iterations 2.8461476E-03 7.4282646E-02 at 120iterations finished qdiffx linear iterations at : 20:43:51 total time elapsed so far: 11.59000 # loops : 120 mean,max change (kT/e) : 2.8461476E-03 7.4282646E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 20:43:51 11.757u 0.460s 0:12.54 97.3% 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 20:43:52 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5082 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.562954 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): 1.872000 64.37800 ymin,ymax (A): -7.714000 54.61100 zmin,zma (A): -1.135000 59.96300 x,y,z range (A): 62.50600 62.32500 61.09800 scale (grids/A): 2.562954 object centre (A): 33.12500 23.44850 29.41400 number of atom coordinates read : 5082 total number of charged atoms : 4928 net assigned charge : 3.121028 assigned positive charge : 780.3818 centred at (gu) : 82.65682 85.08828 87.66364 assigned negative charge : -777.2664 centred at (gu) : 82.18814 84.99265 87.49654 start vw surface at 0.1700000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 274823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39513 grid for indexing accessible points = 1.400000 m= 140888 mr = 208382 m= 47735 mr = 115737 m= 9630 mr = 37584 m= 992 mr = 6742 m= 26 mr = 539 m= 0 mr = 0 time to grow re-entrant surface = 1.570000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.450000 number of dielectric boundary points 105110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 39396 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) : 1.708636 object centre at (A) : 33.12500 23.44850 29.41400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4805174 7.8575082E-02 midg,1,midg; midg,igrid,midg -8.2186654E-02 0.1005359 1,midg,midg; igrid,midg,midg 4.7391420E-03 0.8888355 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 2.820000 now iterating at: 20:43:55 rms-change max change #iterations 12.86009 421.5412 at 10iterations 7.659463 150.5081 at 20iterations 4.539758 78.08812 at 30iterations 2.678110 55.90366 at 40iterations 1.575001 26.63151 at 50iterations 0.9241987 14.87350 at 60iterations 0.5391576 11.94972 at 70iterations 0.3151925 4.933479 at 80iterations 0.1836368 2.972619 at 90iterations 0.1071389 1.670982 at 100iterations 6.2638015E-02 1.038681 at 110iterations 3.6640704E-02 0.5845337 at 120iterations 2.1671923E-02 0.3326492 at 130iterations 1.3011405E-02 0.2028046 at 140iterations 8.0843568E-03 0.1320190 at 150iterations 5.2902396E-03 9.1031075E-02 at 160iterations 3.6993963E-03 5.6467056E-02 at 170iterations 2.7828529E-03 4.1728973E-02 at 180iterations finished qdiffx linear iterations at : 20:44:12 total time elapsed so far: 20.11000 # loops : 180 mean,max change (kT/e) : 2.7828529E-03 4.1728973E-02 energy calculations done at 20.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.27000 DelPhi exited at 20:44:13 20.278u 0.505s 0:21.14 98.2% 0+0k 0+0io 0pf+0w