Sun Oct 9 08:19:54 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 Sun Oct 9 2011 at 08:19:54 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 = 6164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4658771 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 0.4658771 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.999985 assigned positive charge : 929.0333 centred at (gu) : 89.89520 88.79507 89.27026 assigned negative charge : -931.0417 centred at (gu) : 89.83174 88.78958 89.14186 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 124650 no. pairs analyzed = 124650 no. exposed pairs = 7746 no. arc points = 53117 no. surface atoms = 2588 nbur = 3576 mkacc time = 0.3600000 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 = 1.820000 m= 221 mr = 4035 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 4293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4869 ## 918 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 11155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0509112E-11 4.0183301E-11 midg,1,midg; midg,igrid,midg -6.9715783E-12 -3.0072586E-13 1,midg,midg; igrid,midg,midg -3.0152970E-11 2.2737028E-11 gauss-seidel spectral radius is 0.9765567 estimated iterations to convergence 54 setup time was (sec) 0.9500000 now iterating at: 08:19:55 rms-change max change #iterations 4.6756782E-02 12.25699 at 10iterations 2.1690577E-03 0.4625549 at 20iterations 2.4676599E-04 6.9534302E-02 at 30iterations 6.2438732E-05 1.8087387E-02 at 40iterations 1.7853714E-05 4.9934387E-03 at 50iterations finished qdiffx linear iterations at : 08:19:59 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.7853714E-05 4.9934387E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 08:19:59 4.454u 0.263s 0:04.99 94.3% 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 Sun Oct 9 2011 at 08:19:59 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 = 6164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2200000 grid size : 179 scale,in grids/A, set to be: 1.397631 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 1.397631 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.999985 assigned positive charge : 929.0333 centred at (gu) : 89.68398 86.38355 87.80837 assigned negative charge : -931.0417 centred at (gu) : 89.49519 86.36865 87.42525 start vw surface at 0.3100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 94058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 23699 mr = 63769 m= 1464 mr = 14668 m= 18 mr = 461 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 789 time to turn everything in is 0.9300000 number of dielectric boundary points 40341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 952 ## 22 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 43370 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) : 0.4658771 object centre at (A) : 42.08350 54.00550 38.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9162190E-03 4.5439987E-03 midg,1,midg; midg,igrid,midg -1.1340519E-03 -1.1754312E-03 1,midg,midg; igrid,midg,midg -6.5940591E-03 -7.1543446E-03 gauss-seidel spectral radius is 0.9978035 estimated iterations to convergence 170 setup time was (sec) 1.230000 now iterating at: 08:20:01 rms-change max change #iterations 3.520481 136.5409 at 10iterations 1.346661 50.15164 at 20iterations 0.5165884 16.78275 at 30iterations 0.1973239 6.558018 at 40iterations 7.5602613E-02 2.834409 at 50iterations 2.8971290E-02 1.001989 at 60iterations 1.1137580E-02 0.3494568 at 70iterations 4.2830226E-03 0.1408581 at 80iterations 1.6412447E-03 5.1403046E-02 at 90iterations 6.3381199E-04 2.0423889E-02 at 100iterations 2.4481790E-04 8.1272125E-03 at 110iterations 9.5296688E-05 3.2419264E-03 at 120iterations finished qdiffx linear iterations at : 08:20:09 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 9.5296688E-05 3.2419264E-03 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 08:20:09 9.743u 0.301s 0:10.36 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 Sun Oct 9 2011 at 08:20:10 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 = 6164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.096447 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 2.096447 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.999985 assigned positive charge : 929.0333 centred at (gu) : 89.52572 84.57463 86.71200 assigned negative charge : -931.0417 centred at (gu) : 89.24269 84.55277 86.13789 start vw surface at 0.2600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 220158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 90649 mr = 158177 m= 18132 mr = 68367 m= 1613 mr = 12059 m= 42 mr = 802 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 2716 time to turn everything in is 2.050000 number of dielectric boundary points 91189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 47594 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) : 1.397631 object centre at (A) : 42.08350 54.00550 38.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1074598 5.0362699E-02 midg,1,midg; midg,igrid,midg -6.1919601E-03 -1.0109203E-02 1,midg,midg; igrid,midg,midg -1.4196482E-02 -0.5980629 gauss-seidel spectral radius is 0.9991007 estimated iterations to convergence 263 setup time was (sec) 2.390000 now iterating at: 08:20:12 rms-change max change #iterations 10.29199 310.5609 at 10iterations 5.824908 129.8395 at 20iterations 3.277979 78.50697 at 30iterations 1.833217 40.40763 at 40iterations 1.019530 21.80842 at 50iterations 0.5653261 11.44388 at 60iterations 0.3126201 6.165535 at 70iterations 0.1724704 3.536629 at 80iterations 9.4780229E-02 1.961715 at 90iterations 5.2025020E-02 0.9668274 at 100iterations 2.8590621E-02 0.5282903 at 110iterations 1.5693752E-02 0.3000424 at 120iterations 8.5874489E-03 0.1704216 at 130iterations 4.7024968E-03 9.6540451E-02 at 140iterations 2.5666761E-03 5.1186800E-02 at 150iterations 1.4056534E-03 2.6125431E-02 at 160iterations 7.6980831E-04 1.4625549E-02 at 170iterations 4.2191049E-04 8.2855225E-03 at 180iterations finished qdiffx linear iterations at : 08:20:26 total time elapsed so far: 16.32000 # loops : 180 mean,max change (kT/e) : 4.2191049E-04 8.2855225E-03 energy calculations done at 16.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 08:20:27 16.500u 0.302s 0:17.15 97.9% 0+0k 0+0io 0pf+0w