Sat Oct 8 17:47:47 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 17:47:47 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3500 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5240535 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): 2.8999925E-02 44.70900 ymin,ymax (A): -30.45300 26.14900 zmin,zma (A): 1.397000 69.32900 x,y,z range (A): 44.68000 56.60200 67.93200 scale (grids/A): 0.5240535 object centre (A): 22.36900 -2.151999 35.36300 number of atom coordinates read : 3500 total number of charged atoms : 3353 net assigned charge : -5.871982 assigned positive charge : 535.4742 centred at (gu) : 90.23802 91.80440 90.63384 assigned negative charge : -541.3478 centred at (gu) : 90.19788 91.75291 90.63148 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6102 nv = 96 ne = 84 npr = 71505 no. pairs analyzed = 71505 no. exposed pairs = 4350 no. arc points = 29416 no. surface atoms = 1475 nbur = 2025 mkacc time = 0.1500000 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 = 1.624000 m= 204 mr = 3204 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3033 ## 468 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3750019E-10 -1.6974312E-10 midg,1,midg; midg,igrid,midg -2.0936902E-10 4.1261168E-11 1,midg,midg; igrid,midg,midg -2.7421629E-10 -1.6556376E-11 gauss-seidel spectral radius is 0.9812773 estimated iterations to convergence 60 setup time was (sec) 0.6000000 now iterating at: 17:47:48 rms-change max change #iterations 6.7028776E-02 11.48430 at 10iterations 4.1131615E-03 0.6708622 at 20iterations 3.8648542E-04 6.9854736E-02 at 30iterations 8.4764339E-05 1.5966415E-02 at 40iterations 2.3068233E-05 4.3220520E-03 at 50iterations finished qdiffx linear iterations at : 17:47:50 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.3068233E-05 4.3220520E-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 17:47:51 3.357u 0.173s 0:03.81 92.3% 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 Sat Oct 8 2011 at 17:47:51 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3500 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.572160 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): 2.8999925E-02 44.70900 ymin,ymax (A): -30.45300 26.14900 zmin,zma (A): 1.397000 69.32900 x,y,z range (A): 44.68000 56.60200 67.93200 scale (grids/A): 1.572160 object centre (A): 22.36900 -2.151999 35.36300 number of atom coordinates read : 3500 total number of charged atoms : 3353 net assigned charge : -5.871982 assigned positive charge : 535.4742 centred at (gu) : 90.71336 95.41258 91.90030 assigned negative charge : -541.3478 centred at (gu) : 90.59323 95.25803 91.89405 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20425 mr = 47540 m= 1814 mr = 13757 m= 49 mr = 796 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 341 time to turn everything in is 0.5000000 number of dielectric boundary points 28790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 25348 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) : 0.5240535 object centre at (A) : 22.36900 -2.151999 35.36300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6183840E-03 9.8594157E-03 midg,1,midg; midg,igrid,midg -8.8075968E-03 -1.1246470E-02 1,midg,midg; igrid,midg,midg -4.5774537E-03 1.4798518E-03 gauss-seidel spectral radius is 0.9980771 estimated iterations to convergence 181 setup time was (sec) 0.7700000 now iterating at: 17:47:52 rms-change max change #iterations 3.395654 178.6750 at 10iterations 1.380789 59.37741 at 20iterations 0.5595891 21.25778 at 30iterations 0.2289706 8.975708 at 40iterations 9.2382312E-02 3.484596 at 50iterations 3.7884966E-02 1.394537 at 60iterations 1.5491825E-02 0.5778656 at 70iterations 6.3098716E-03 0.2352180 at 80iterations 2.6003725E-03 9.8770142E-02 at 90iterations 1.0800584E-03 3.6117345E-02 at 100iterations 4.6514760E-04 1.6301155E-02 at 110iterations 2.1002184E-04 7.4732304E-03 at 120iterations finished qdiffx linear iterations at : 17:47:58 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 2.1002184E-04 7.4732304E-03 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 17:47:59 7.365u 0.229s 0:07.87 96.3% 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 Sat Oct 8 2011 at 17:47:59 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3500 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.358241 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): 2.8999925E-02 44.70900 ymin,ymax (A): -30.45300 26.14900 zmin,zma (A): 1.397000 69.32900 x,y,z range (A): 44.68000 56.60200 67.93200 scale (grids/A): 2.358241 object centre (A): 22.36900 -2.151999 35.36300 number of atom coordinates read : 3500 total number of charged atoms : 3353 net assigned charge : -5.871982 assigned positive charge : 535.4742 centred at (gu) : 91.06973 98.11864 92.85025 assigned negative charge : -541.3478 centred at (gu) : 90.88982 97.88705 92.84101 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 160009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72752 mr = 116742 m= 18804 mr = 57317 m= 2553 mr = 13665 m= 141 mr = 1525 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1170 time to turn everything in is 1.170000 number of dielectric boundary points 64960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 26747 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) : 1.572160 object centre at (A) : 22.36900 -2.151999 35.36300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1793020 7.8901142E-02 midg,1,midg; midg,igrid,midg -0.1269643 -0.1558204 1,midg,midg; igrid,midg,midg -7.8372873E-02 4.6437308E-02 gauss-seidel spectral radius is 0.9991100 estimated iterations to convergence 265 setup time was (sec) 1.480000 now iterating at: 17:48:00 rms-change max change #iterations 9.042846 262.9046 at 10iterations 5.024112 113.5039 at 20iterations 2.779459 63.28974 at 30iterations 1.529780 41.79018 at 40iterations 0.8400090 17.67793 at 50iterations 0.4588814 9.881461 at 60iterations 0.2511566 5.328825 at 70iterations 0.1368741 2.970062 at 80iterations 7.4812979E-02 1.471306 at 90iterations 4.0808808E-02 0.8905113 at 100iterations 2.2204574E-02 0.4637585 at 110iterations 1.2112516E-02 0.2480545 at 120iterations 6.6211303E-03 0.1306496 at 130iterations 3.6130419E-03 7.5326979E-02 at 140iterations 1.9743526E-03 4.0626526E-02 at 150iterations 1.0824746E-03 2.1669388E-02 at 160iterations 6.0017372E-04 1.2490273E-02 at 170iterations 3.3571749E-04 6.3171387E-03 at 180iterations finished qdiffx linear iterations at : 17:48:10 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 3.3571749E-04 6.3171387E-03 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 17:48:11 11.884u 0.234s 0:12.38 97.8% 0+0k 0+0io 0pf+0w