Mon Oct 10 10:24:35 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 Mon Oct 10 2011 at 10:24:35 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 = 2741 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: 0.5615585 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 0.5615585 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.000017 assigned positive charge : 398.9552 centred at (gu) : 91.22617 90.60315 86.61235 assigned negative charge : -389.9555 centred at (gu) : 91.42244 90.58244 86.49062 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5763 nv = 96 ne = 84 npr = 53093 no. pairs analyzed = 53093 no. exposed pairs = 4169 no. arc points = 29948 no. surface atoms = 1382 nbur = 1359 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 = 1.540000 m= 273 mr = 2500 m= 0 mr = 5 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 3531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9848559E-10 1.0280555E-09 midg,1,midg; midg,igrid,midg 7.5148032E-10 1.4781444E-09 1,midg,midg; igrid,midg,midg 2.2396440E-09 -1.3109730E-09 gauss-seidel spectral radius is 0.9836373 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 10:24:36 rms-change max change #iterations 7.9139359E-02 15.98166 at 10iterations 5.4633482E-03 1.070982 at 20iterations 4.2072139E-04 7.1680069E-02 at 30iterations 4.3286254E-05 7.0672035E-03 at 40iterations 7.7917994E-06 1.1591911E-03 at 50iterations finished qdiffx linear iterations at : 10:24:39 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 7.7917994E-06 1.1591911E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 10:24:39 3.682u 0.198s 0:04.16 93.0% 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 Mon Oct 10 2011 at 10:24:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 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: 1.684676 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 1.684676 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.000017 assigned positive charge : 398.9552 centred at (gu) : 93.67831 91.80905 79.83691 assigned negative charge : -389.9555 centred at (gu) : 94.26717 91.74701 79.47174 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29948 grid for indexing accessible points = 1.400000 m= 19034 mr = 37522 m= 2244 mr = 11874 m= 71 mr = 931 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.4900000 number of dielectric boundary points 32781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20014 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) : 0.5615585 object centre at (A) : 11.31050 17.32700 25.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3063671E-05 7.8415014E-03 midg,1,midg; midg,igrid,midg 1.2067659E-02 1.6608533E-02 1,midg,midg; igrid,midg,midg 1.4908878E-02 -2.1207489E-02 gauss-seidel spectral radius is 0.9982859 estimated iterations to convergence 192 setup time was (sec) 0.8000000 now iterating at: 10:24:40 rms-change max change #iterations 3.305430 165.6560 at 10iterations 1.404918 55.14849 at 20iterations 0.5956134 24.30179 at 30iterations 0.2532751 9.894459 at 40iterations 0.1079533 4.544950 at 50iterations 4.6219733E-02 2.029610 at 60iterations 1.9657124E-02 0.7753582 at 70iterations 8.3617484E-03 0.3259330 at 80iterations 3.5622227E-03 0.1280880 at 90iterations 1.5209619E-03 6.0523987E-02 at 100iterations 6.4926449E-04 2.2617340E-02 at 110iterations 2.7826088E-04 1.0276794E-02 at 120iterations finished qdiffx linear iterations at : 10:24:47 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 2.7826088E-04 1.0276794E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 10:24:48 8.114u 0.248s 0:08.63 96.7% 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 Mon Oct 10 2011 at 10:24:48 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 = 2741 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: 2.527013 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 2.527013 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.000017 assigned positive charge : 398.9552 centred at (gu) : 95.51720 92.71346 74.75530 assigned negative charge : -389.9555 centred at (gu) : 96.40080 92.62044 74.20757 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29948 grid for indexing accessible points = 1.400000 m= 63223 mr = 92716 m= 19634 mr = 46730 m= 3464 mr = 13841 m= 266 mr = 1987 m= 7 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 1.180000 number of dielectric boundary points 73958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 20747 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) : 1.684676 object centre at (A) : 11.31050 17.32700 25.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8772207E-03 9.3238190E-02 midg,1,midg; midg,igrid,midg 0.1995877 0.2135663 1,midg,midg; igrid,midg,midg 0.2427753 -0.6368139 gauss-seidel spectral radius is 0.9991751 estimated iterations to convergence 275 setup time was (sec) 1.510000 now iterating at: 10:24:50 rms-change max change #iterations 8.805759 297.0176 at 10iterations 5.153919 142.9792 at 20iterations 2.984626 102.6060 at 30iterations 1.700494 48.03130 at 40iterations 0.9683251 24.24504 at 50iterations 0.5454984 15.98711 at 60iterations 0.3078005 8.150839 at 70iterations 0.1730597 5.763347 at 80iterations 9.7464204E-02 2.384218 at 90iterations 5.4447092E-02 1.198603 at 100iterations 3.0489514E-02 0.7612915 at 110iterations 1.7070070E-02 0.3773804 at 120iterations 9.5067788E-03 0.2116451 at 130iterations 5.3035645E-03 0.1180840 at 140iterations 2.9658824E-03 6.3514709E-02 at 150iterations 1.6561401E-03 4.2008400E-02 at 160iterations 9.2317694E-04 1.9934416E-02 at 170iterations 5.1480054E-04 1.0979250E-02 at 180iterations finished qdiffx linear iterations at : 10:25:01 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 5.1480054E-04 1.0979250E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 10:25:01 12.868u 0.333s 0:13.63 96.7% 0+0k 0+0io 0pf+0w