Sat Oct 8 11:36:04 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 11:36:05 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 = 5134 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: 0.5414943 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 0.5414943 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4966 net assigned charge : 4.4882298E-05 assigned positive charge : 778.9881 centred at (gu) : 90.36363 90.51482 90.80598 assigned negative charge : -778.9933 centred at (gu) : 90.28212 90.52193 90.86410 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9286 nv = 96 ne = 84 npr = 107771 no. pairs analyzed = 107771 no. exposed pairs = 5970 no. arc points = 40746 no. surface atoms = 2007 nbur = 3127 mkacc time = 0.3200000 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 = 1.596000 m= 360 mr = 5101 m= 0 mr = 9 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.6600000 number of dielectric boundary points 4536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4178 ## 528 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 12550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6475071E-10 -7.0358952E-10 midg,1,midg; midg,igrid,midg 6.3560046E-11 -7.6784690E-11 1,midg,midg; igrid,midg,midg -7.3584816E-10 8.7248830E-10 gauss-seidel spectral radius is 0.9825663 estimated iterations to convergence 62 setup time was (sec) 0.9300000 now iterating at: 11:36:06 rms-change max change #iterations 9.5390290E-02 16.74368 at 10iterations 8.0443127E-03 1.377258 at 20iterations 1.4827593E-03 0.3467941 at 30iterations 4.0757825E-04 9.1865540E-02 at 40iterations 1.1840099E-04 2.5459290E-02 at 50iterations finished qdiffx linear iterations at : 11:36:09 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.1840099E-04 2.5459290E-02 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 11:36:09 4.260u 0.159s 0:04.89 90.1% 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 11:36:09 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 = 5134 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: 1.624483 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 1.624483 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4966 net assigned charge : 4.4882298E-05 assigned positive charge : 778.9881 centred at (gu) : 91.08942 91.54266 92.41647 assigned negative charge : -778.9933 centred at (gu) : 90.84578 91.56556 92.59202 start vw surface at 0.2700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 104505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32273 mr = 74075 m= 3288 mr = 22424 m= 75 mr = 1532 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 752 time to turn everything in is 0.9200000 number of dielectric boundary points 42105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 37982 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) : 0.5414943 object centre at (A) : 40.17800 35.16300 42.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3178075E-02 -8.0388058E-03 midg,1,midg; midg,igrid,midg -7.7566970E-03 -2.6757619E-04 1,midg,midg; igrid,midg,midg -8.9389337E-03 7.2772815E-03 gauss-seidel spectral radius is 0.9983660 estimated iterations to convergence 196 setup time was (sec) 1.270000 now iterating at: 11:36:11 rms-change max change #iterations 4.522697 184.9153 at 10iterations 1.970686 62.04361 at 20iterations 0.8600918 25.36963 at 30iterations 0.3765256 10.78172 at 40iterations 0.1647842 4.765680 at 50iterations 7.2005130E-02 1.948616 at 60iterations 3.1814426E-02 0.8814430 at 70iterations 1.4092768E-02 0.3928947 at 80iterations 6.3341232E-03 0.1867676 at 90iterations 2.9322854E-03 9.6191406E-02 at 100iterations 1.4197134E-03 5.4153442E-02 at 110iterations 7.4137194E-04 2.7084351E-02 at 120iterations finished qdiffx linear iterations at : 11:36:19 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 7.4137194E-04 2.7084351E-02 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 11:36:19 9.324u 0.224s 0:09.83 97.0% 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 Sat Oct 8 2011 at 11:36:19 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 = 5134 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: 2.436724 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 2.436724 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4966 net assigned charge : 4.4882298E-05 assigned positive charge : 778.9881 centred at (gu) : 91.63387 92.31363 93.62431 assigned negative charge : -778.9933 centred at (gu) : 91.26865 92.34816 93.88783 start vw surface at 0.2700000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 243539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 112323 mr = 181553 m= 32232 mr = 89263 m= 5022 mr = 24217 m= 326 mr = 3256 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 1.350000 no. cavity mid-points inaccessible to solvent = 2614 time to turn everything in is 2.290000 number of dielectric boundary points 95022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 39675 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) : 1.624483 object centre at (A) : 40.17800 35.16300 42.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3381999 -0.2839215 midg,1,midg; midg,igrid,midg -0.1561857 -6.3522361E-02 1,midg,midg; igrid,midg,midg -0.1895817 -4.6546184E-02 gauss-seidel spectral radius is 0.9992405 estimated iterations to convergence 286 setup time was (sec) 2.670000 now iterating at: 11:36:22 rms-change max change #iterations 11.85899 295.6902 at 10iterations 7.019246 167.0192 at 20iterations 4.139131 78.35046 at 30iterations 2.419930 46.36247 at 40iterations 1.411265 26.83172 at 50iterations 0.8223362 16.49155 at 60iterations 0.4762913 9.698307 at 70iterations 0.2759654 5.382146 at 80iterations 0.1594458 2.939173 at 90iterations 9.2074335E-02 1.684456 at 100iterations 5.3323772E-02 1.033245 at 110iterations 3.0757001E-02 0.6072235 at 120iterations 1.7741941E-02 0.3015509 at 130iterations 1.0270569E-02 0.2131805 at 140iterations 5.9608240E-03 0.1064978 at 150iterations 3.4744409E-03 6.2538147E-02 at 160iterations 2.0488335E-03 3.6766052E-02 at 170iterations 1.2234548E-03 2.3635864E-02 at 180iterations finished qdiffx linear iterations at : 11:36:36 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 1.2234548E-03 2.3635864E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.31000 DelPhi exited at 11:36:36 16.309u 0.199s 0:16.80 98.1% 0+0k 0+0io 0pf+0w