Tue Oct 11 03:14:52 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 Tue Oct 11 2011 at 03:14:52 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 = 3130 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: 0.5966847 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 0.5966847 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2991 net assigned charge : -6.999979 assigned positive charge : 465.1219 centred at (gu) : 90.60939 91.47429 91.78507 assigned negative charge : -472.1229 centred at (gu) : 90.54113 91.46272 91.78552 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7217 nv = 96 ne = 84 npr = 65473 no. pairs analyzed = 65473 no. exposed pairs = 3837 no. arc points = 26555 no. surface atoms = 1304 nbur = 1826 mkacc time = 0.1800000 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 = 1.456000 m= 328 mr = 3919 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9178 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8152637E-09 -4.0453942E-09 midg,1,midg; midg,igrid,midg -2.2825211E-09 -3.0969287E-09 1,midg,midg; igrid,midg,midg -4.7363944E-09 1.6862244E-11 gauss-seidel spectral radius is 0.9855049 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 03:14:53 rms-change max change #iterations 0.1153722 19.59396 at 10iterations 9.6865995E-03 1.358932 at 20iterations 8.9875708E-04 0.1371803 at 30iterations 1.2641918E-04 1.9911677E-02 at 40iterations 3.0727857E-05 5.7347417E-03 at 50iterations finished qdiffx linear iterations at : 03:14:56 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.0727857E-05 5.7347417E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 03:14:57 4.009u 0.265s 0:04.75 89.6% 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 Tue Oct 11 2011 at 03:14:57 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 = 3130 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: 1.790054 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 1.790054 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2991 net assigned charge : -6.999979 assigned positive charge : 465.1219 centred at (gu) : 91.82744 94.42191 95.35405 assigned negative charge : -472.1229 centred at (gu) : 91.62303 94.38785 95.35635 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26555 grid for indexing accessible points = 1.400000 m= 26633 mr = 54168 m= 3602 mr = 19296 m= 124 mr = 2104 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 0.6800000 number of dielectric boundary points 33275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 23286 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) : 0.5966847 object centre at (A) : 22.74600 106.8775 131.7015 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1285741E-03 1.6601611E-02 midg,1,midg; midg,igrid,midg 3.8596101E-02 -8.1187505E-03 1,midg,midg; igrid,midg,midg -2.1610506E-02 -5.3086840E-03 gauss-seidel spectral radius is 0.9985037 estimated iterations to convergence 205 setup time was (sec) 0.9700000 now iterating at: 03:14:58 rms-change max change #iterations 4.127699 184.0553 at 10iterations 1.858511 68.70782 at 20iterations 0.8411625 31.78611 at 30iterations 0.3792892 14.74190 at 40iterations 0.1712814 5.627911 at 50iterations 7.7485897E-02 2.484247 at 60iterations 3.5071712E-02 1.110512 at 70iterations 1.5851567E-02 0.5039520 at 80iterations 7.2016609E-03 0.2529006 at 90iterations 3.2716144E-03 9.8991871E-02 at 100iterations 1.4908653E-03 4.5804024E-02 at 110iterations 6.8806019E-04 2.2521973E-02 at 120iterations finished qdiffx linear iterations at : 03:15:07 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 6.8806019E-04 2.2521973E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 03:15:07 9.274u 0.283s 0:10.13 94.2% 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 Tue Oct 11 2011 at 03:15:07 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 = 3130 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: 2.685081 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 2.685081 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2991 net assigned charge : -6.999979 assigned positive charge : 465.1219 centred at (gu) : 92.74080 96.63279 98.03089 assigned negative charge : -472.1229 centred at (gu) : 92.43430 96.58167 98.03441 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 182314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26555 grid for indexing accessible points = 1.400000 m= 88296 mr = 132138 m= 29186 mr = 71446 m= 6105 mr = 23084 m= 646 mr = 4456 m= 13 mr = 396 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 2087 time to turn everything in is 1.710000 number of dielectric boundary points 75038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 23917 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) : 1.790054 object centre at (A) : 22.74600 106.8775 131.7015 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9025623E-02 0.7743590 midg,1,midg; midg,igrid,midg 0.8304487 -0.2982014 1,midg,midg; igrid,midg,midg -0.2939638 -4.3812163E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 2.040000 now iterating at: 03:15:10 rms-change max change #iterations 10.11689 290.6353 at 10iterations 5.895563 145.9393 at 20iterations 3.411532 76.16683 at 30iterations 1.961119 40.16103 at 40iterations 1.128621 20.16810 at 50iterations 0.6465510 12.51036 at 60iterations 0.3698946 8.744920 at 70iterations 0.2114172 4.002850 at 80iterations 0.1209063 2.379333 at 90iterations 6.9000840E-02 1.199529 at 100iterations 3.9393619E-02 0.7570925 at 110iterations 2.2487298E-02 0.4145470 at 120iterations 1.2844342E-02 0.2622325 at 130iterations 7.3325429E-03 0.1305573 at 140iterations 4.1917977E-03 7.8268528E-02 at 150iterations 2.4115432E-03 4.9148560E-02 at 160iterations 1.3900474E-03 2.6246548E-02 at 170iterations 8.0908235E-04 1.6260147E-02 at 180iterations finished qdiffx linear iterations at : 03:15:23 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 8.0908235E-04 1.6260147E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 03:15:24 15.655u 0.300s 0:16.71 95.4% 0+0k 0+0io 0pf+0w