Sat Oct 8 21:39:17 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 21:39:18 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 = 2025 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6656072 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 0.6656072 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 87.81940 89.33430 89.62189 assigned negative charge : -300.5609 centred at (gu) : 87.93990 89.37969 89.65928 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6049 nv = 96 ne = 84 npr = 40807 no. pairs analyzed = 40807 no. exposed pairs = 2554 no. arc points = 18238 no. surface atoms = 869 nbur = 1156 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3302 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4531425E-09 -6.6384493E-09 midg,1,midg; midg,igrid,midg 8.4666061E-09 -7.4858200E-09 1,midg,midg; igrid,midg,midg 3.2391004E-08 -1.4004128E-08 gauss-seidel spectral radius is 0.9882487 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 21:39:18 rms-change max change #iterations 0.1456097 20.80900 at 10iterations 1.5717197E-02 2.609615 at 20iterations 1.6876679E-03 0.2457657 at 30iterations 1.8695186E-04 2.8152466E-02 at 40iterations 2.4352201E-05 3.7536621E-03 at 50iterations finished qdiffx linear iterations at : 21:39:21 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.4352201E-05 3.7536621E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 21:39:21 3.270u 0.205s 0:03.83 90.6% 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 Sat Oct 8 2011 at 21:39:21 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 = 2025 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.996822 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 1.996822 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 83.45816 88.00274 88.86546 assigned negative charge : -300.5609 centred at (gu) : 83.81974 88.13908 88.97779 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18238 grid for indexing accessible points = 1.400000 m= 23630 mr = 44785 m= 4158 mr = 17132 m= 264 mr = 2592 m= 1 mr = 78 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 0.4700000 number of dielectric boundary points 28505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14952 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) : 0.6656072 object centre at (A) : 32.99550 26.46950 34.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0191219E-02 -2.1922830E-03 midg,1,midg; midg,igrid,midg 2.6954185E-02 2.2047954E-03 1,midg,midg; igrid,midg,midg -3.7218291E-02 -4.5691337E-02 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 0.7600000 now iterating at: 21:39:22 rms-change max change #iterations 4.010543 182.3287 at 10iterations 1.913001 68.65716 at 20iterations 0.9051756 30.20863 at 30iterations 0.4334869 17.19236 at 40iterations 0.2058195 6.808958 at 50iterations 9.8212779E-02 3.272209 at 60iterations 4.6804864E-02 1.645268 at 70iterations 2.2182636E-02 0.7303848 at 80iterations 1.0615768E-02 0.3493423 at 90iterations 5.0699273E-03 0.1668973 at 100iterations 2.4199367E-03 8.6068630E-02 at 110iterations 1.1566592E-03 3.6767006E-02 at 120iterations finished qdiffx linear iterations at : 21:39:29 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 1.1566592E-03 3.6767006E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 21:39:29 7.438u 0.234s 0:07.97 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 Sat Oct 8 2011 at 21:39:29 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 = 2025 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.995232 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 2.995232 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 80.18721 87.00417 88.29811 assigned negative charge : -300.5609 centred at (gu) : 80.72961 87.20861 88.46661 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 150295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18238 grid for indexing accessible points = 1.400000 m= 75756 mr = 108242 m= 28474 mr = 61707 m= 7475 mr = 22714 m= 1198 mr = 5606 m= 51 mr = 756 m= 0 mr = 5 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 64219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 15111 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) : 1.996822 object centre at (A) : 32.99550 26.46950 34.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1202649 -1.7937105E-02 midg,1,midg; midg,igrid,midg 0.2451668 -5.5436231E-02 1,midg,midg; igrid,midg,midg -0.5884727 -0.6871395 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.550000 now iterating at: 21:39:31 rms-change max change #iterations 9.337376 378.1382 at 10iterations 5.499123 125.9052 at 20iterations 3.212542 69.61436 at 30iterations 1.873255 41.35967 at 40iterations 1.090941 24.79467 at 50iterations 0.6327395 14.38400 at 60iterations 0.3673907 7.946059 at 70iterations 0.2131451 4.100571 at 80iterations 0.1229996 2.410168 at 90iterations 7.1091585E-02 1.574184 at 100iterations 4.1030783E-02 0.7711391 at 110iterations 2.3700584E-02 0.4544702 at 120iterations 1.3679999E-02 0.2681141 at 130iterations 7.9056509E-03 0.1487579 at 140iterations 4.5634178E-03 9.6492767E-02 at 150iterations 2.6408418E-03 5.0342560E-02 at 160iterations 1.5325109E-03 2.9501915E-02 at 170iterations 8.9225231E-04 1.7836571E-02 at 180iterations finished qdiffx linear iterations at : 21:39:41 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 8.9225231E-04 1.7836571E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 21:39:42 11.922u 0.211s 0:12.42 97.6% 0+0k 0+0io 0pf+0w