Sat Oct 8 14:53:19 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 Sat Oct 8 2011 at 14:53:19 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6388630 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 0.6388630 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.242007 assigned positive charge : 448.5806 centred at (gu) : 88.79306 90.00078 91.76996 assigned negative charge : -447.3394 centred at (gu) : 88.71665 89.85678 91.75247 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8053 nv = 96 ne = 84 npr = 62657 no. pairs analyzed = 62657 no. exposed pairs = 3327 no. arc points = 23520 no. surface atoms = 1137 nbur = 1853 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4695 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6403374E-10 6.0279444E-09 midg,1,midg; midg,igrid,midg -1.7119993E-08 2.0236763E-08 1,midg,midg; igrid,midg,midg -1.0658075E-08 9.0056060E-09 gauss-seidel spectral radius is 0.9873358 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 14:53:19 rms-change max change #iterations 0.1615451 21.51517 at 10iterations 1.5908882E-02 2.137984 at 20iterations 1.6347534E-03 0.2181778 at 30iterations 1.8365469E-04 2.2729874E-02 at 40iterations 2.3661098E-05 3.1261444E-03 at 50iterations finished qdiffx linear iterations at : 14:53:22 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.3661098E-05 3.1261444E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:53:22 3.113u 0.142s 0:03.53 92.0% 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 Sat Oct 8 2011 at 14:53:22 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.916589 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 1.916589 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.242007 assigned positive charge : 448.5806 centred at (gu) : 86.37846 90.00159 95.30948 assigned negative charge : -447.3394 centred at (gu) : 86.14980 89.56999 95.25729 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23520 grid for indexing accessible points = 1.400000 m= 31897 mr = 63828 m= 4754 mr = 24064 m= 269 mr = 2920 m= 4 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.5900000 number of dielectric boundary points 34338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 22379 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) : 0.6388630 object centre at (A) : 15.62400 -0.5594997 19.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7325340E-03 9.0291249E-03 midg,1,midg; midg,igrid,midg 3.0042138E-04 2.8424133E-02 1,midg,midg; igrid,midg,midg -3.4948736E-02 2.3501100E-02 gauss-seidel spectral radius is 0.9986829 estimated iterations to convergence 218 setup time was (sec) 0.8600000 now iterating at: 14:53:23 rms-change max change #iterations 4.688952 183.4053 at 10iterations 2.232609 63.62880 at 20iterations 1.060916 31.48120 at 30iterations 0.5043975 14.41524 at 40iterations 0.2392615 7.420773 at 50iterations 0.1137390 3.375883 at 60iterations 5.4125916E-02 1.546935 at 70iterations 2.5766840E-02 0.7931976 at 80iterations 1.2267662E-02 0.3513408 at 90iterations 5.8270218E-03 0.1835098 at 100iterations 2.7657696E-03 7.5624466E-02 at 110iterations 1.3224962E-03 3.9744854E-02 at 120iterations finished qdiffx linear iterations at : 14:53:29 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 1.3224962E-03 3.9744854E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 14:53:30 7.019u 0.159s 0:07.44 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 Sat Oct 8 2011 at 14:53:30 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.874883 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): -12.23800 43.48600 ymin,ymax (A): -23.91200 22.79300 zmin,zma (A): -7.573000 47.53600 x,y,z range (A): 55.72400 46.70500 55.10900 scale (grids/A): 2.874883 object centre (A): 15.62400 -0.5594997 19.98150 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.242007 assigned positive charge : 448.5806 centred at (gu) : 84.56746 90.00230 97.96428 assigned negative charge : -447.3394 centred at (gu) : 84.22469 89.35488 97.88579 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 204885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23520 grid for indexing accessible points = 1.400000 m= 104450 mr = 154243 m= 36486 mr = 87107 m= 8432 mr = 29546 m= 1167 mr = 6170 m= 64 mr = 778 m= 0 mr = 24 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1439 time to turn everything in is 1.500000 number of dielectric boundary points 77616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 22759 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) : 1.916589 object centre at (A) : 15.62400 -0.5594997 19.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6014976E-02 0.2415115 midg,1,midg; midg,igrid,midg 7.8525292E-03 0.3160258 1,midg,midg; igrid,midg,midg -0.4479115 0.3510410 gauss-seidel spectral radius is 0.9992743 estimated iterations to convergence 293 setup time was (sec) 1.770000 now iterating at: 14:53:32 rms-change max change #iterations 10.89017 403.8470 at 10iterations 6.368101 143.6015 at 20iterations 3.704815 69.99036 at 30iterations 2.156512 39.04007 at 40iterations 1.249237 22.66141 at 50iterations 0.7253956 12.48540 at 60iterations 0.4200450 6.899898 at 70iterations 0.2426867 4.181079 at 80iterations 0.1403030 2.209851 at 90iterations 8.1349544E-02 1.345616 at 100iterations 4.6988674E-02 0.8392048 at 110iterations 2.7172068E-02 0.4898071 at 120iterations 1.5706439E-02 0.2561951 at 130iterations 9.0910867E-03 0.1572638 at 140iterations 5.2554263E-03 8.9084625E-02 at 150iterations 3.0456400E-03 4.7893524E-02 at 160iterations 1.7692531E-03 3.1408072E-02 at 170iterations 1.0318119E-03 1.6077995E-02 at 180iterations finished qdiffx linear iterations at : 14:53:41 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 1.0318119E-03 1.6077995E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 14:53:42 11.399u 0.171s 0:11.84 97.6% 0+0k 0+0io 0pf+0w