Sun Oct 9 19:54:48 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 19:54:48 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3557 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5669422 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): 6.513999 68.23100 ymin,ymax (A): 1.718000 61.95600 zmin,zma (A): -0.9130000 61.88000 x,y,z range (A): 61.71700 60.23800 62.79300 scale (grids/A): 0.5669422 object centre (A): 37.37250 31.83700 30.48350 number of atom coordinates read : 3557 total number of charged atoms : 3407 net assigned charge : -1.378969 assigned positive charge : 538.9965 centred at (gu) : 88.36884 88.49683 88.45936 assigned negative charge : -540.3774 centred at (gu) : 88.28399 88.56298 88.44434 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7716 nv = 96 ne = 84 npr = 68581 no. pairs analyzed = 68581 no. exposed pairs = 4737 no. arc points = 32848 no. surface atoms = 1601 nbur = 1956 mkacc time = 0.1200000 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 = 1.540000 m= 413 mr = 4032 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3229 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2450844E-10 5.3085928E-11 midg,1,midg; midg,igrid,midg 1.3682241E-09 -9.1447633E-10 1,midg,midg; igrid,midg,midg -2.4368045E-09 8.4520163E-10 gauss-seidel spectral radius is 0.9840029 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 19:54:49 rms-change max change #iterations 9.8474398E-02 16.38769 at 10iterations 7.6063229E-03 1.258034 at 20iterations 1.1922680E-03 0.1532516 at 30iterations 6.3410116E-04 7.2770119E-02 at 40iterations 3.9513843E-04 4.6504974E-02 at 50iterations finished qdiffx linear iterations at : 19:54:52 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.9513843E-04 4.6504974E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:54:52 3.381u 0.181s 0:03.90 91.2% 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 19:54:52 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3557 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.700827 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): 6.513999 68.23100 ymin,ymax (A): 1.718000 61.95600 zmin,zma (A): -0.9130000 61.88000 x,y,z range (A): 61.71700 60.23800 62.79300 scale (grids/A): 1.700827 object centre (A): 37.37250 31.83700 30.48350 number of atom coordinates read : 3557 total number of charged atoms : 3407 net assigned charge : -1.378969 assigned positive charge : 538.9965 centred at (gu) : 85.10556 85.48938 85.37728 assigned negative charge : -540.3774 centred at (gu) : 84.85141 85.68861 85.33266 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 84876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32848 grid for indexing accessible points = 1.400000 m= 29201 mr = 57911 m= 3994 mr = 20238 m= 161 mr = 2108 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 0.4000000 number of dielectric boundary points 37955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 26288 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) : 0.5669422 object centre at (A) : 37.37250 31.83700 30.48350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9817214E-02 -7.1759811E-03 midg,1,midg; midg,igrid,midg 1.1556054E-02 -4.6280120E-03 1,midg,midg; igrid,midg,midg -9.0921633E-03 3.9522555E-03 gauss-seidel spectral radius is 0.9983972 estimated iterations to convergence 198 setup time was (sec) 0.6200000 now iterating at: 19:54:53 rms-change max change #iterations 4.106400 167.4288 at 10iterations 1.801316 64.07686 at 20iterations 0.7928303 27.22107 at 30iterations 0.3499616 11.26181 at 40iterations 0.1540472 5.061391 at 50iterations 6.7982145E-02 2.060989 at 60iterations 3.0053176E-02 0.9675217 at 70iterations 1.3427375E-02 0.4132458 at 80iterations 6.1459579E-03 0.2108624 at 90iterations 3.0840398E-03 9.2665672E-02 at 100iterations 1.8252678E-03 5.6561470E-02 at 110iterations 1.3181757E-03 3.8166046E-02 at 120iterations finished qdiffx linear iterations at : 19:55:00 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.3181757E-03 3.8166046E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 19:55:00 7.764u 0.196s 0:08.23 96.5% 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 19:55:01 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3557 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.551240 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): 6.513999 68.23100 ymin,ymax (A): 1.718000 61.95600 zmin,zma (A): -0.9130000 61.88000 x,y,z range (A): 61.71700 60.23800 62.79300 scale (grids/A): 2.551240 object centre (A): 37.37250 31.83700 30.48350 number of atom coordinates read : 3557 total number of charged atoms : 3407 net assigned charge : -1.378969 assigned positive charge : 538.9965 centred at (gu) : 82.65810 83.23392 83.06566 assigned negative charge : -540.3774 centred at (gu) : 82.27695 83.53291 82.99886 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 196928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32848 grid for indexing accessible points = 1.400000 m= 96962 mr = 141623 m= 31998 mr = 76747 m= 6625 mr = 24356 m= 648 mr = 4451 m= 17 mr = 301 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 509 time to turn everything in is 1.040000 number of dielectric boundary points 85700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 27241 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) : 1.700827 object centre at (A) : 37.37250 31.83700 30.48350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1277930 2.3661604E-02 midg,1,midg; midg,igrid,midg 0.1577966 -6.9783196E-02 1,midg,midg; igrid,midg,midg -2.2738045E-02 2.8941135E-03 gauss-seidel spectral radius is 0.9992225 estimated iterations to convergence 283 setup time was (sec) 1.270000 now iterating at: 19:55:02 rms-change max change #iterations 10.67386 324.0666 at 10iterations 6.336290 166.3370 at 20iterations 3.719064 84.74403 at 30iterations 2.165333 45.19261 at 40iterations 1.256749 33.19010 at 50iterations 0.7238910 15.42164 at 60iterations 0.4177300 8.254786 at 70iterations 0.2395204 4.616901 at 80iterations 0.1373742 2.643913 at 90iterations 7.8834541E-02 1.731160 at 100iterations 4.5038763E-02 1.001503 at 110iterations 2.5728606E-02 0.4900513 at 120iterations 1.4703534E-02 0.2718239 at 130iterations 8.3726449E-03 0.1790869 at 140iterations 4.7782920E-03 9.5376968E-02 at 150iterations 2.7280604E-03 5.1595926E-02 at 160iterations 1.5674507E-03 3.2143593E-02 at 170iterations 9.0573879E-04 1.6365051E-02 at 180iterations finished qdiffx linear iterations at : 19:55:13 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 9.0573879E-04 1.6365051E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 19:55:14 12.880u 0.201s 0:13.35 97.9% 0+0k 0+0io 0pf+0w