Sat Oct 8 18:21:16 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 Sat Oct 8 2011 at 18:21:16 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 = 3759 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: 0.5506403 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 0.5506403 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3609 net assigned charge : -7.999969 assigned positive charge : 566.6863 centred at (gu) : 89.13580 86.73627 90.50845 assigned negative charge : -574.6887 centred at (gu) : 89.20055 86.71852 90.50475 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7433 nv = 96 ne = 84 npr = 75892 no. pairs analyzed = 75892 no. exposed pairs = 4888 no. arc points = 34338 no. surface atoms = 1625 nbur = 2134 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 = 1.568000 m= 310 mr = 3832 m= 0 mr = 13 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3471 ## 460 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5409671E-10 -6.2163691E-10 midg,1,midg; midg,igrid,midg -1.7097699E-09 -1.9430893E-10 1,midg,midg; igrid,midg,midg 7.9241690E-11 -1.0088015E-09 gauss-seidel spectral radius is 0.9830548 estimated iterations to convergence 63 setup time was (sec) 0.7300000 now iterating at: 18:21:17 rms-change max change #iterations 8.4642164E-02 14.64848 at 10iterations 6.0958867E-03 0.8481865 at 20iterations 5.6641741E-04 9.7892761E-02 at 30iterations 1.2469872E-04 2.3388863E-02 at 40iterations 3.7569556E-05 7.2011948E-03 at 50iterations finished qdiffx linear iterations at : 18:21:20 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 3.7569556E-05 7.2011948E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 18:21:20 4.205u 0.250s 0:04.77 93.2% 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 18:21:20 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 = 3759 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: 1.651921 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 1.651921 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3609 net assigned charge : -7.999969 assigned positive charge : 566.6863 centred at (gu) : 87.40617 80.20769 91.52441 assigned negative charge : -574.6887 centred at (gu) : 87.60123 80.15525 91.51381 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25835 mr = 55750 m= 2820 mr = 17433 m= 74 mr = 1345 m= 0 mr = 5 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 36352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 27737 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) : 0.5506403 object centre at (A) : 28.55800 12.92400 26.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4140216E-03 -3.3613907E-03 midg,1,midg; midg,igrid,midg -2.7688442E-02 -6.9754017E-03 1,midg,midg; igrid,midg,midg -7.3637795E-03 -3.3388749E-02 gauss-seidel spectral radius is 0.9983011 estimated iterations to convergence 193 setup time was (sec) 1.020000 now iterating at: 18:21:22 rms-change max change #iterations 3.904477 149.1756 at 10iterations 1.666994 59.13014 at 20iterations 0.7163733 26.92764 at 30iterations 0.3075919 9.672772 at 40iterations 0.1320254 4.338868 at 50iterations 5.6483917E-02 1.767624 at 60iterations 2.4211654E-02 0.8118345 at 70iterations 1.0414533E-02 0.3672562 at 80iterations 4.5077396E-03 0.1445212 at 90iterations 1.9491337E-03 6.2797546E-02 at 100iterations 8.5899181E-04 2.9699802E-02 at 110iterations 3.8810959E-04 1.2277126E-02 at 120iterations finished qdiffx linear iterations at : 18:21:30 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 3.8810959E-04 1.2277126E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 18:21:31 9.587u 0.315s 0:10.20 96.9% 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 18:21:31 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 = 3759 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: 2.477882 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 2.477882 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3609 net assigned charge : -7.999969 assigned positive charge : 566.6863 centred at (gu) : 86.10898 75.31098 92.28648 assigned negative charge : -574.6887 centred at (gu) : 86.40172 75.23284 92.27065 start vw surface at 0.1800000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 190722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89202 mr = 136281 m= 25663 mr = 69928 m= 4316 mr = 19076 m= 324 mr = 2710 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 82138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 28845 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) : 1.651921 object centre at (A) : 28.55800 12.92400 26.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5026514E-04 0.1089405 midg,1,midg; midg,igrid,midg -0.4027960 -9.4069347E-02 1,midg,midg; igrid,midg,midg -0.1316807 -0.6241069 gauss-seidel spectral radius is 0.9991899 estimated iterations to convergence 277 setup time was (sec) 2.150000 now iterating at: 18:21:33 rms-change max change #iterations 10.06163 308.9797 at 10iterations 5.763283 116.4787 at 20iterations 3.296980 66.65350 at 30iterations 1.868073 37.36971 at 40iterations 1.058051 21.53520 at 50iterations 0.5969689 12.00684 at 60iterations 0.3355274 6.668324 at 70iterations 0.1886554 3.438111 at 80iterations 0.1061617 1.974419 at 90iterations 5.9529815E-02 1.083981 at 100iterations 3.3450976E-02 0.6660981 at 110iterations 1.8761672E-02 0.3382359 at 120iterations 1.0507439E-02 0.2093201 at 130iterations 5.9124734E-03 0.1115265 at 140iterations 3.3333746E-03 6.6626072E-02 at 150iterations 1.8817538E-03 3.9052963E-02 at 160iterations 1.0702171E-03 2.1008968E-02 at 170iterations 6.1734969E-04 1.1940002E-02 at 180iterations finished qdiffx linear iterations at : 18:21:47 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 6.1734969E-04 1.1940002E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 18:21:48 16.252u 0.315s 0:16.85 98.2% 0+0k 0+0io 0pf+0w