Mon Oct 10 14:08:21 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 14:08:21 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 = 4471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5769200 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 0.5769200 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.999957 assigned positive charge : 671.1101 centred at (gu) : 90.20048 87.72222 88.57323 assigned negative charge : -674.1132 centred at (gu) : 90.12062 87.81277 88.66975 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9521 nv = 96 ne = 84 npr = 94436 no. pairs analyzed = 94436 no. exposed pairs = 4943 no. arc points = 33445 no. surface atoms = 1684 nbur = 2787 mkacc time = 0.3100000 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 = 1.484000 m= 419 mr = 5598 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.6200000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3549 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 12535 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0503380E-09 -2.5864071E-09 midg,1,midg; midg,igrid,midg 3.4640366E-09 -2.0154083E-09 1,midg,midg; igrid,midg,midg -2.9668086E-09 1.7468162E-09 gauss-seidel spectral radius is 0.9845982 estimated iterations to convergence 66 setup time was (sec) 0.9100000 now iterating at: 14:08:22 rms-change max change #iterations 0.1224612 16.43602 at 10iterations 9.7400006E-03 1.363407 at 20iterations 8.9146075E-04 0.1175079 at 30iterations 1.5601968E-04 1.8029056E-02 at 40iterations 5.1742474E-05 6.8489313E-03 at 50iterations finished qdiffx linear iterations at : 14:08:26 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 5.1742474E-05 6.8489313E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 14:08:27 4.684u 0.409s 0:05.49 92.5% 0+0k 0+0io 6pf+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 14:08:27 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 = 4471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.730760 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 1.730760 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.999957 assigned positive charge : 671.1101 centred at (gu) : 90.60069 83.16540 85.71817 assigned negative charge : -674.1132 centred at (gu) : 90.36111 83.43802 86.00870 start vw surface at 0.2100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 106309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33445 grid for indexing accessible points = 1.400000 m= 36422 mr = 77882 m= 4655 mr = 27092 m= 193 mr = 2950 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2447 time to turn everything in is 1.050000 number of dielectric boundary points 39616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 33466 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) : 0.5769200 object centre at (A) : 4.772500 68.61350 60.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7876354E-03 -2.5578324E-02 midg,1,midg; midg,igrid,midg 4.2873714E-02 3.4942099E-05 1,midg,midg; igrid,midg,midg -6.7359013E-03 3.0093838E-02 gauss-seidel spectral radius is 0.9985107 estimated iterations to convergence 205 setup time was (sec) 1.400000 now iterating at: 14:08:28 rms-change max change #iterations 4.770092 178.1812 at 10iterations 2.157860 60.55103 at 20iterations 0.9783363 26.34362 at 30iterations 0.4446927 14.02143 at 40iterations 0.2018395 5.720120 at 50iterations 9.1791451E-02 2.410997 at 60iterations 4.1598640E-02 1.211388 at 70iterations 1.8978165E-02 0.5048447 at 80iterations 8.6115757E-03 0.2393329 at 90iterations 3.9379462E-03 9.8420143E-02 at 100iterations 1.7943089E-03 5.4359436E-02 at 110iterations 8.3222555E-04 2.3918152E-02 at 120iterations finished qdiffx linear iterations at : 14:08:38 total time elapsed so far: 11.00000 # loops : 120 mean,max change (kT/e) : 8.3222555E-04 2.3918152E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 14:08:39 11.223u 0.436s 0:12.05 96.6% 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 Mon Oct 10 2011 at 14:08:39 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 = 4471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.596140 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 2.596140 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.999957 assigned positive charge : 671.1101 centred at (gu) : 90.90075 79.74791 83.57696 assigned negative charge : -674.1132 centred at (gu) : 90.54148 80.15688 84.01299 start vw surface at 0.2100000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 247471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33445 grid for indexing accessible points = 1.400000 m= 123363 mr = 188934 m= 39344 mr = 102566 m= 8058 mr = 31608 m= 821 mr = 6119 m= 20 mr = 510 m= 0 mr = 2 time to grow re-entrant surface = 1.630000 no. cavity mid-points inaccessible to solvent = 8438 time to turn everything in is 2.660000 number of dielectric boundary points 89338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.820000 number of grid points assigned charge 34520 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) : 1.730760 object centre at (A) : 4.772500 68.61350 60.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1104252 -0.3031138 midg,1,midg; midg,igrid,midg 0.6227871 0.2350445 1,midg,midg; igrid,midg,midg -0.2408773 0.2813455 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 3.030000 now iterating at: 14:08:42 rms-change max change #iterations 11.62923 312.5490 at 10iterations 6.810726 134.0472 at 20iterations 3.946815 71.09126 at 30iterations 2.291057 38.07782 at 40iterations 1.320546 22.71125 at 50iterations 0.7620364 12.18292 at 60iterations 0.4395137 7.336849 at 70iterations 0.2524443 4.100351 at 80iterations 0.1452205 2.432917 at 90iterations 8.3312958E-02 1.405388 at 100iterations 4.7958244E-02 0.7454243 at 110iterations 2.7584286E-02 0.4332829 at 120iterations 1.5874043E-02 0.2408733 at 130iterations 9.1545088E-03 0.1440697 at 140iterations 5.2924217E-03 8.8047504E-02 at 150iterations 3.0861334E-03 4.8188210E-02 at 160iterations 1.8253407E-03 3.1481743E-02 at 170iterations 1.1069441E-03 1.7860353E-02 at 180iterations finished qdiffx linear iterations at : 14:08:58 total time elapsed so far: 18.82000 # loops : 180 mean,max change (kT/e) : 1.1069441E-03 1.7860353E-02 energy calculations done at 18.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.03000 DelPhi exited at 14:08:59 19.037u 0.490s 0:19.86 98.2% 0+0k 0+0io 0pf+0w