Mon Oct 10 16:20:35 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 16:20:35 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 = 2481 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: 0.6229222 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): 60.74900 115.6040 ymin,ymax (A): 229.5270 286.6770 zmin,zma (A): 84.63800 127.3830 x,y,z range (A): 54.85500 57.14999 42.74500 scale (grids/A): 0.6229222 object centre (A): 88.17650 258.1020 106.0105 number of atom coordinates read : 2481 total number of charged atoms : 2341 net assigned charge : 8.500022 assigned positive charge : 374.6737 centred at (gu) : 89.36878 88.61932 90.19862 assigned negative charge : -366.1746 centred at (gu) : 89.18662 88.50533 90.30945 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 48357 no. pairs analyzed = 48357 no. exposed pairs = 3428 no. arc points = 25655 no. surface atoms = 1134 nbur = 1347 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3079 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3100000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4516224E-08 5.9058175E-11 midg,1,midg; midg,igrid,midg -3.7014317E-10 1.1404285E-08 1,midg,midg; igrid,midg,midg -5.7603295E-09 1.7299760E-08 gauss-seidel spectral radius is 0.9866524 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 16:20:36 rms-change max change #iterations 0.1235625 18.91710 at 10iterations 1.1386546E-02 1.666821 at 20iterations 1.0572177E-03 0.1515369 at 30iterations 9.7569937E-05 1.5598297E-02 at 40iterations 9.0115118E-06 1.3856888E-03 at 50iterations finished qdiffx linear iterations at : 16:20:39 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 9.0115118E-06 1.3856888E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 16:20:39 3.325u 0.186s 0:03.79 92.3% 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 16:20:39 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 = 2481 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.868767 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): 60.74900 115.6040 ymin,ymax (A): 229.5270 286.6770 zmin,zma (A): 84.63800 127.3830 x,y,z range (A): 54.85500 57.14999 42.74500 scale (grids/A): 1.868767 object centre (A): 88.17650 258.1020 106.0105 number of atom coordinates read : 2481 total number of charged atoms : 2341 net assigned charge : 8.500022 assigned positive charge : 374.6737 centred at (gu) : 88.10578 85.85733 90.59520 assigned negative charge : -366.1746 centred at (gu) : 87.55982 85.51579 90.92821 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 67740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 grid for indexing accessible points = 1.400000 m= 24493 mr = 42999 m= 4396 mr = 17200 m= 265 mr = 2798 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 170 time to turn everything in is 0.5300000 number of dielectric boundary points 33809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18322 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) : 0.6229222 object centre at (A) : 88.17650 258.1020 106.0105 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5951362E-02 -5.7767336E-03 midg,1,midg; midg,igrid,midg 1.5429398E-02 3.3612057E-04 1,midg,midg; igrid,midg,midg 1.1729047E-02 3.5096761E-02 gauss-seidel spectral radius is 0.9985833 estimated iterations to convergence 211 setup time was (sec) 0.8100000 now iterating at: 16:20:40 rms-change max change #iterations 3.950624 196.0103 at 10iterations 1.806511 66.45575 at 20iterations 0.8324037 30.03885 at 30iterations 0.3835049 14.56511 at 40iterations 0.1762904 6.093271 at 50iterations 8.1184149E-02 2.721419 at 60iterations 3.7356824E-02 1.290600 at 70iterations 1.7137814E-02 0.6312065 at 80iterations 7.8903269E-03 0.2934980 at 90iterations 3.6449134E-03 0.1252122 at 100iterations 1.6812080E-03 5.3182602E-02 at 110iterations 7.7294186E-04 2.3742676E-02 at 120iterations finished qdiffx linear iterations at : 16:20:47 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 7.7294186E-04 2.3742676E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 16:20:48 8.218u 0.251s 0:08.81 96.0% 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 16:20:48 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 = 2481 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: 2.803150 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): 60.74900 115.6040 ymin,ymax (A): 229.5270 286.6770 zmin,zma (A): 84.63800 127.3830 x,y,z range (A): 54.85500 57.14999 42.74500 scale (grids/A): 2.803150 object centre (A): 88.17650 258.1020 106.0105 number of atom coordinates read : 2481 total number of charged atoms : 2341 net assigned charge : 8.500022 assigned positive charge : 374.6737 centred at (gu) : 87.15839 83.78596 90.89261 assigned negative charge : -366.1746 centred at (gu) : 86.33959 83.27364 91.39218 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 156137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 grid for indexing accessible points = 1.400000 m= 75841 mr = 105107 m= 30332 mr = 59459 m= 8069 mr = 23970 m= 1163 mr = 6013 m= 74 mr = 796 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 505 time to turn everything in is 1.230000 number of dielectric boundary points 76245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 18718 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) : 1.868767 object centre at (A) : 88.17650 258.1020 106.0105 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1718290 -4.5678355E-02 midg,1,midg; midg,igrid,midg 0.2302549 -0.6948633 1,midg,midg; igrid,midg,midg 0.1043635 0.3221340 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.540000 now iterating at: 16:20:50 rms-change max change #iterations 9.465714 327.5287 at 10iterations 5.545243 145.9812 at 20iterations 3.211214 70.88544 at 30iterations 1.854427 47.48194 at 40iterations 1.070092 25.54321 at 50iterations 0.6141450 12.13263 at 60iterations 0.3524103 7.261694 at 70iterations 0.2023434 3.673683 at 80iterations 0.1159134 2.168608 at 90iterations 6.6592842E-02 1.259750 at 100iterations 3.8089294E-02 0.7920623 at 110iterations 2.1791235E-02 0.4725218 at 120iterations 1.2489228E-02 0.2522240 at 130iterations 7.1421773E-03 0.1400123 at 140iterations 4.0992503E-03 8.6505890E-02 at 150iterations 2.3478251E-03 4.6482086E-02 at 160iterations 1.3403040E-03 2.5140047E-02 at 170iterations 7.6772296E-04 1.4904022E-02 at 180iterations finished qdiffx linear iterations at : 16:21:00 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 7.6772296E-04 1.4904022E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 16:21:01 12.077u 0.223s 0:12.59 97.6% 0+0k 0+0io 0pf+0w