Sun Oct 9 08:54:23 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+sph2.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 = amb2.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 08:54:23 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: HIR 697 has a net charge of 0.5140 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: 0.5134492 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 0.5134492 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.985973 assigned positive charge : 851.0089 centred at (gu) : 89.84826 89.45683 88.98753 assigned negative charge : -857.0017 centred at (gu) : 89.77336 89.51433 89.01584 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9600 nv = 96 ne = 84 npr = 113121 no. pairs analyzed = 113121 no. exposed pairs = 7158 no. arc points = 49131 no. surface atoms = 2396 nbur = 3261 mkacc time = 0.2400000 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 = 1.652000 m= 344 mr = 5006 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4835 ## 701 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6842612E-12 -1.5227052E-10 midg,1,midg; midg,igrid,midg 1.1886148E-10 -2.6161476E-10 1,midg,midg; igrid,midg,midg -3.7862963E-10 1.5565836E-10 gauss-seidel spectral radius is 0.9806666 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 08:54:24 rms-change max change #iterations 7.6680206E-02 9.975956 at 10iterations 4.5771450E-03 0.7142596 at 20iterations 5.3736760E-04 0.1174202 at 30iterations 1.6279944E-04 3.7651062E-02 at 40iterations 5.6274723E-05 1.2613297E-02 at 50iterations finished qdiffx linear iterations at : 08:54:26 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 5.6274723E-05 1.2613297E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:54:27 3.506u 0.200s 0:04.01 92.2% 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 08:54:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: HIR 697 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.540348 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 1.540348 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.985973 assigned positive charge : 851.0089 centred at (gu) : 89.54313 88.36849 86.96080 assigned negative charge : -857.0017 centred at (gu) : 89.31973 88.54308 87.04716 start vw surface at 0.2600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 108307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49131 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32094 mr = 74695 m= 2730 mr = 21324 m= 34 mr = 1144 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1028 time to turn everything in is 0.7800000 number of dielectric boundary points 46002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 674 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 41326 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) : 0.5134492 object centre at (A) : 42.85250 18.66250 16.03200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3128793E-03 -2.1022230E-02 midg,1,midg; midg,igrid,midg 1.3564305E-03 -4.4490765E-03 1,midg,midg; igrid,midg,midg -2.1587053E-02 2.4115825E-03 gauss-seidel spectral radius is 0.9982224 estimated iterations to convergence 188 setup time was (sec) 1.080000 now iterating at: 08:54:28 rms-change max change #iterations 4.262487 155.8486 at 10iterations 1.793084 51.16965 at 20iterations 0.7519965 22.15468 at 30iterations 0.3166009 9.502072 at 40iterations 0.1336436 3.690042 at 50iterations 5.6393806E-02 1.719641 at 60iterations 2.3743937E-02 0.7947311 at 70iterations 1.0048991E-02 0.2722297 at 80iterations 4.2784689E-03 0.1252499 at 90iterations 1.8374937E-03 5.3012848E-02 at 100iterations 8.0854219E-04 2.4548531E-02 at 110iterations 3.7729021E-04 1.4990807E-02 at 120iterations finished qdiffx linear iterations at : 08:54:36 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 3.7729021E-04 1.4990807E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 08:54:36 8.740u 0.227s 0:09.24 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 08:54:36 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: HIR 697 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.310521 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 2.310521 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.985973 assigned positive charge : 851.0089 centred at (gu) : 89.31441 87.55239 85.44091 assigned negative charge : -857.0017 centred at (gu) : 88.97948 87.81471 85.57062 start vw surface at 0.2100000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 251940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49131 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 114636 mr = 183239 m= 29131 mr = 89520 m= 3946 mr = 20802 m= 214 mr = 2374 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 3295 time to turn everything in is 1.780000 number of dielectric boundary points 103867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 43791 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) : 1.540348 object centre at (A) : 42.85250 18.66250 16.03200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2505561 -0.5206628 midg,1,midg; midg,igrid,midg 6.0781162E-02 -6.6987790E-02 1,midg,midg; igrid,midg,midg -0.6515492 4.0889375E-02 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 2.120000 now iterating at: 08:54:38 rms-change max change #iterations 11.56048 306.4909 at 10iterations 6.811446 155.0177 at 20iterations 3.980785 90.74057 at 30iterations 2.308608 45.45134 at 40iterations 1.334772 26.26103 at 50iterations 0.7702134 17.06081 at 60iterations 0.4426050 8.626955 at 70iterations 0.2537406 4.922409 at 80iterations 0.1450573 2.652041 at 90iterations 8.2889549E-02 1.629326 at 100iterations 4.7325585E-02 0.9472218 at 110iterations 2.7008241E-02 0.4499226 at 120iterations 1.5404817E-02 0.3033485 at 130iterations 8.7726507E-03 0.1728287 at 140iterations 5.0002853E-03 9.2578888E-02 at 150iterations 2.8480997E-03 5.0075531E-02 at 160iterations 1.6261031E-03 2.9754639E-02 at 170iterations 9.3276025E-04 1.5117645E-02 at 180iterations finished qdiffx linear iterations at : 08:54:49 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 9.3276025E-04 1.5117645E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 08:54:50 13.248u 0.228s 0:13.77 97.7% 0+0k 0+0io 0pf+0w