Mon Oct 10 14:05:19 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 Mon Oct 10 2011 at 14:05:19 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5249808 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 0.5249808 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 491.7977 centred at (gu) : 88.53812 88.35253 90.37582 assigned negative charge : -491.2989 centred at (gu) : 88.45248 88.40823 90.27863 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5770 nv = 96 ne = 84 npr = 63438 no. pairs analyzed = 63438 no. exposed pairs = 4250 no. arc points = 30231 no. surface atoms = 1436 nbur = 1774 mkacc time = 0.1100000 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 = 1.624000 m= 254 mr = 2833 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3016 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7566646E-10 3.5616643E-10 midg,1,midg; midg,igrid,midg 2.9553610E-10 -1.0929314E-10 1,midg,midg; igrid,midg,midg -3.9119846E-10 1.9650429E-10 gauss-seidel spectral radius is 0.9813334 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 14:05:20 rms-change max change #iterations 6.3263603E-02 10.56641 at 10iterations 4.3534865E-03 0.7269440 at 20iterations 5.9945363E-04 0.1013279 at 30iterations 1.4332894E-04 2.4318695E-02 at 40iterations 3.6380112E-05 6.3648224E-03 at 50iterations finished qdiffx linear iterations at : 14:05:23 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.6380112E-05 6.3648224E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:05:23 3.395u 0.159s 0:03.92 90.3% 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 Mon Oct 10 2011 at 14:05:23 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.574943 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 1.574943 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 491.7977 centred at (gu) : 85.61355 85.05657 91.12643 assigned negative charge : -491.2989 centred at (gu) : 85.35701 85.22431 90.83546 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19460 mr = 42060 m= 2105 mr = 12936 m= 50 mr = 972 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 139 time to turn everything in is 0.3200000 number of dielectric boundary points 29512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23346 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) : 0.5249808 object centre at (A) : 19.05500 8.720999 8.789000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0697761E-03 3.2365490E-02 midg,1,midg; midg,igrid,midg 9.3521585E-04 -8.5011832E-03 1,midg,midg; igrid,midg,midg -1.0766086E-02 4.5250260E-04 gauss-seidel spectral radius is 0.9980727 estimated iterations to convergence 181 setup time was (sec) 0.5300000 now iterating at: 14:05:24 rms-change max change #iterations 3.239882 167.8440 at 10iterations 1.313242 54.47792 at 20iterations 0.5328293 21.63294 at 30iterations 0.2149636 7.725445 at 40iterations 8.7496981E-02 3.222833 at 50iterations 3.5660226E-02 1.523430 at 60iterations 1.4539615E-02 0.5693531 at 70iterations 5.9842672E-03 0.2397461 at 80iterations 2.5123535E-03 0.1005478 at 90iterations 1.0990825E-03 4.3125153E-02 at 100iterations 5.0883752E-04 2.0202637E-02 at 110iterations 2.5759003E-04 1.0848999E-02 at 120iterations finished qdiffx linear iterations at : 14:05:31 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 2.5759003E-04 1.0848999E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 14:05:31 7.605u 0.184s 0:08.21 94.7% 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 14:05:31 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.362414 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 2.362414 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 491.7977 centred at (gu) : 83.42021 82.58462 91.68938 assigned negative charge : -491.2989 centred at (gu) : 83.03538 82.83640 91.25305 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 147961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 67176 mr = 103044 m= 19348 mr = 51978 m= 3257 mr = 13938 m= 208 mr = 2082 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 541 time to turn everything in is 0.7700000 number of dielectric boundary points 66847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24544 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) : 1.574943 object centre at (A) : 19.05500 8.720999 8.789000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0570894E-02 0.5856506 midg,1,midg; midg,igrid,midg 1.5058086E-02 -0.1508801 1,midg,midg; igrid,midg,midg -0.1656099 -4.9610203E-03 gauss-seidel spectral radius is 0.9991060 estimated iterations to convergence 264 setup time was (sec) 1.000000 now iterating at: 14:05:33 rms-change max change #iterations 8.731200 279.4503 at 10iterations 4.896023 150.0804 at 20iterations 2.719337 78.98981 at 30iterations 1.502846 35.03178 at 40iterations 0.8264389 20.22658 at 50iterations 0.4528764 11.07155 at 60iterations 0.2476534 5.224322 at 70iterations 0.1355387 3.120460 at 80iterations 7.3872961E-02 1.684021 at 90iterations 4.0234901E-02 0.8537369 at 100iterations 2.1913862E-02 0.4612732 at 110iterations 1.1941187E-02 0.2652903 at 120iterations 6.5125464E-03 0.1433620 at 130iterations 3.5583240E-03 7.9094887E-02 at 140iterations 1.9487602E-03 4.5524597E-02 at 150iterations 1.0756891E-03 2.3216248E-02 at 160iterations 6.0036744E-04 1.2428284E-02 at 170iterations 3.4136663E-04 7.7781677E-03 at 180iterations finished qdiffx linear iterations at : 14:05:44 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 3.4136663E-04 7.7781677E-03 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 14:05:44 12.134u 0.205s 0:12.85 95.9% 0+0k 0+0io 0pf+0w