Sun Oct 9 15:49:28 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 15:49:28 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5321535 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 0.5321535 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.0262 centred at (gu) : 90.53838 89.93736 89.05324 assigned negative charge : -825.9331 centred at (gu) : 90.47292 89.98944 88.94205 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9524 nv = 96 ne = 84 npr = 109666 no. pairs analyzed = 109666 no. exposed pairs = 6342 no. arc points = 44057 no. surface atoms = 2137 nbur = 3235 mkacc time = 0.1900000 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= 381 mr = 5206 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3600000 number of dielectric boundary points 4682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4348 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1697832E-09 5.4668003E-10 midg,1,midg; midg,igrid,midg 2.8248559E-10 -4.7057480E-10 1,midg,midg; igrid,midg,midg -5.0271837E-10 4.3001311E-10 gauss-seidel spectral radius is 0.9819703 estimated iterations to convergence 61 setup time was (sec) 0.5500000 now iterating at: 15:49:29 rms-change max change #iterations 8.9541741E-02 11.29267 at 10iterations 8.5254516E-03 1.352291 at 20iterations 2.8289335E-03 0.4820976 at 30iterations 1.2180087E-03 0.2093582 at 40iterations 5.2806473E-04 9.1114044E-02 at 50iterations finished qdiffx linear iterations at : 15:49:32 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 5.2806473E-04 9.1114044E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:49:32 3.596u 0.186s 0:04.09 92.1% 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 Sun Oct 9 2011 at 15:49:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.596460 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 1.596460 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.0262 centred at (gu) : 91.61298 89.81042 87.15785 assigned negative charge : -825.9331 centred at (gu) : 91.41865 89.96793 86.82615 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 107594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33610 mr = 76353 m= 3296 mr = 23164 m= 75 mr = 1459 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1826 time to turn everything in is 0.5300000 number of dielectric boundary points 43598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 532 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 39546 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) : 0.5321535 object centre at (A) : 71.56600 75.77200 1.219999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9203098E-02 1.8003517E-03 midg,1,midg; midg,igrid,midg -4.1780644E-03 -1.6578594E-02 1,midg,midg; igrid,midg,midg -1.2043594E-02 1.8636573E-02 gauss-seidel spectral radius is 0.9983187 estimated iterations to convergence 194 setup time was (sec) 0.7500000 now iterating at: 15:49:33 rms-change max change #iterations 4.543684 172.2645 at 10iterations 1.960167 56.18043 at 20iterations 0.8465483 24.51588 at 30iterations 0.3640247 9.920103 at 40iterations 0.1581887 4.616840 at 50iterations 6.8518206E-02 2.235489 at 60iterations 3.0338362E-02 0.8539467 at 70iterations 1.3764906E-02 0.4136162 at 80iterations 6.7886817E-03 0.2198219 at 90iterations 3.7917760E-03 0.1305466 at 100iterations 2.4088256E-03 9.2678070E-02 at 110iterations 1.6777196E-03 6.2175751E-02 at 120iterations finished qdiffx linear iterations at : 15:49:41 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.6777196E-03 6.2175751E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 15:49:41 8.178u 0.205s 0:08.66 96.6% 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 15:49:41 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.394691 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 2.394691 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.0262 centred at (gu) : 92.41892 89.71519 85.73630 assigned negative charge : -825.9331 centred at (gu) : 92.12792 89.95197 85.23920 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 250821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117042 mr = 186806 m= 32864 mr = 93291 m= 5059 mr = 24321 m= 282 mr = 3086 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 6065 time to turn everything in is 1.290000 number of dielectric boundary points 98475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 41540 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) : 1.596460 object centre at (A) : 71.56600 75.77200 1.219999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1334539 0.1262766 midg,1,midg; midg,igrid,midg -6.7930333E-02 -0.1722947 1,midg,midg; igrid,midg,midg -5.3775564E-02 0.3297140 gauss-seidel spectral radius is 0.9992264 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 15:49:43 rms-change max change #iterations 11.85597 395.5231 at 10iterations 6.902828 165.6214 at 20iterations 3.988865 83.11554 at 30iterations 2.300186 44.73413 at 40iterations 1.317729 23.62711 at 50iterations 0.7530776 13.47417 at 60iterations 0.4310891 7.170052 at 70iterations 0.2455907 4.083321 at 80iterations 0.1400939 2.258129 at 90iterations 7.9829320E-02 1.256878 at 100iterations 4.5520246E-02 0.8600006 at 110iterations 2.5897184E-02 0.4439945 at 120iterations 1.4807357E-02 0.2547302 at 130iterations 8.5208043E-03 0.1501867 at 140iterations 4.9588550E-03 9.9514008E-02 at 150iterations 2.9353951E-03 5.4767609E-02 at 160iterations 1.8099317E-03 3.4248352E-02 at 170iterations 1.1826829E-03 2.4459839E-02 at 180iterations finished qdiffx linear iterations at : 15:49:55 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 1.1826829E-03 2.4459839E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 15:49:55 13.492u 0.227s 0:14.04 97.6% 0+0k 0+0io 0pf+0w