Sun Oct 9 08:35:58 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 08:35:58 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 = 6129 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: 0.4685999 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 0.4685999 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.999965 assigned positive charge : 924.9370 centred at (gu) : 89.91642 90.15408 90.34879 assigned negative charge : -927.9448 centred at (gu) : 89.85683 90.13602 90.45713 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8155 nv = 96 ne = 84 npr = 124240 no. pairs analyzed = 124240 no. exposed pairs = 7605 no. arc points = 52581 no. surface atoms = 2550 nbur = 3579 mkacc time = 0.2100000 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 = 1.820000 m= 237 mr = 4142 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4820 ## 914 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1187699E-11 -6.3952142E-11 midg,1,midg; midg,igrid,midg -1.3347326E-11 3.4453412E-12 1,midg,midg; igrid,midg,midg -3.4812236E-11 2.2324934E-11 gauss-seidel spectral radius is 0.9768234 estimated iterations to convergence 55 setup time was (sec) 0.5800000 now iterating at: 08:35:59 rms-change max change #iterations 4.9333006E-02 8.756203 at 10iterations 2.5399304E-03 0.4766769 at 20iterations 3.6038566E-04 9.2781067E-02 at 30iterations 8.9820671E-05 2.1610260E-02 at 40iterations 2.4903560E-05 5.3710938E-03 at 50iterations finished qdiffx linear iterations at : 08:36:01 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.4903560E-05 5.3710938E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 08:36:02 3.577u 0.165s 0:04.02 92.7% 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 Sun Oct 9 2011 at 08:36:02 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 = 6129 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: 1.405800 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 1.405800 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.999965 assigned positive charge : 924.9370 centred at (gu) : 89.74733 90.46043 91.04455 assigned negative charge : -927.9448 centred at (gu) : 89.57010 90.40773 91.37092 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 93971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 24473 mr = 63855 m= 1560 mr = 15631 m= 26 mr = 508 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1252 time to turn everything in is 0.4600000 number of dielectric boundary points 40036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 892 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 43246 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) : 0.4685999 object centre at (A) : 35.20350 4.468501 61.38300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0642406E-02 -3.2493786E-03 midg,1,midg; midg,igrid,midg -3.1611640E-03 -1.5073518E-03 1,midg,midg; igrid,midg,midg -7.3377644E-03 -1.1787144E-02 gauss-seidel spectral radius is 0.9978322 estimated iterations to convergence 171 setup time was (sec) 0.6800000 now iterating at: 08:36:03 rms-change max change #iterations 3.581660 151.1951 at 10iterations 1.375028 43.69295 at 20iterations 0.5299513 16.78711 at 30iterations 0.2041934 6.783390 at 40iterations 7.8810349E-02 2.574505 at 50iterations 3.0387629E-02 1.030487 at 60iterations 1.1756262E-02 0.3674369 at 70iterations 4.5820703E-03 0.1637516 at 80iterations 1.7862790E-03 5.8006287E-02 at 90iterations 7.1032898E-04 2.4316788E-02 at 100iterations 2.9541852E-04 1.1299133E-02 at 110iterations 1.3150433E-04 5.5637360E-03 at 120iterations finished qdiffx linear iterations at : 08:36:10 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.3150433E-04 5.5637360E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 08:36:10 7.794u 0.204s 0:08.31 96.1% 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 08:36:10 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 = 6129 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.108700 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 2.108700 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.999965 assigned positive charge : 924.9370 centred at (gu) : 89.62033 90.69000 91.56615 assigned negative charge : -927.9448 centred at (gu) : 89.35518 90.61146 92.05633 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 220205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 91440 mr = 158215 m= 19352 mr = 69641 m= 1904 mr = 13457 m= 53 mr = 969 m= 0 mr = 7 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 4243 time to turn everything in is 1.100000 number of dielectric boundary points 90665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 47343 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) : 1.405800 object centre at (A) : 35.20350 4.468501 61.38300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2090312 -7.9745367E-02 midg,1,midg; midg,igrid,midg -5.6811418E-02 -2.7450563E-02 1,midg,midg; igrid,midg,midg -0.1027239 -0.5185181 gauss-seidel spectral radius is 0.9991090 estimated iterations to convergence 265 setup time was (sec) 1.340000 now iterating at: 08:36:12 rms-change max change #iterations 10.29238 341.6074 at 10iterations 5.813950 132.6051 at 20iterations 3.272334 71.70139 at 30iterations 1.827307 36.87192 at 40iterations 1.016739 22.38696 at 50iterations 0.5630402 11.36776 at 60iterations 0.3121558 6.098690 at 70iterations 0.1722652 3.523922 at 80iterations 9.5124610E-02 2.019566 at 90iterations 5.2202020E-02 1.037201 at 100iterations 2.8786989E-02 0.6057320 at 110iterations 1.5814722E-02 0.3127060 at 120iterations 8.6818775E-03 0.1734285 at 130iterations 4.7685434E-03 9.2155457E-02 at 140iterations 2.6169477E-03 4.9886942E-02 at 150iterations 1.4396665E-03 2.9445648E-02 at 160iterations 7.9398917E-04 1.5419006E-02 at 170iterations 4.3871245E-04 8.1441402E-03 at 180iterations finished qdiffx linear iterations at : 08:36:23 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 4.3871245E-04 8.1441402E-03 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 08:36:24 13.012u 0.230s 0:13.70 96.6% 0+0k 0+0io 0pf+0w