Sun Oct 9 15:31:25 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 15:31:25 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 = 5322 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5119503 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): 22.83400 84.49300 ymin,ymax (A): 14.33000 81.37100 zmin,zma (A): -35.81000 33.72800 x,y,z range (A): 61.65900 67.04100 69.53799 scale (grids/A): 0.5119503 object centre (A): 53.66350 47.85050 -1.041002 number of atom coordinates read : 5322 total number of charged atoms : 5152 net assigned charge : -0.8999621 assigned positive charge : 817.8515 centred at (gu) : 90.96346 89.79081 90.49128 assigned negative charge : -818.7583 centred at (gu) : 90.91882 89.82328 90.54181 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8388 nv = 96 ne = 84 npr = 109466 no. pairs analyzed = 109466 no. exposed pairs = 6208 no. arc points = 42098 no. surface atoms = 2125 nbur = 3197 mkacc time = 0.2600000 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= 293 mr = 4498 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.5400000 number of dielectric boundary points 4171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4196 ## 624 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2591277E-10 -1.9908311E-10 midg,1,midg; midg,igrid,midg 9.2407186E-11 -1.1079668E-10 1,midg,midg; igrid,midg,midg -1.2077493E-10 1.6246671E-10 gauss-seidel spectral radius is 0.9805108 estimated iterations to convergence 59 setup time was (sec) 0.7700000 now iterating at: 15:31:26 rms-change max change #iterations 7.5743414E-02 13.50605 at 10iterations 7.2419918E-03 1.241318 at 20iterations 2.1669220E-03 0.3675652 at 30iterations 7.8486238E-04 0.1334953 at 40iterations 2.8547423E-04 4.8591614E-02 at 50iterations finished qdiffx linear iterations at : 15:31:28 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.8547423E-04 4.8591614E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 15:31:29 3.577u 0.148s 0:04.08 90.9% 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 15:31:29 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 = 5322 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.535851 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): 22.83400 84.49300 ymin,ymax (A): 14.33000 81.37100 zmin,zma (A): -35.81000 33.72800 x,y,z range (A): 61.65900 67.04100 69.53799 scale (grids/A): 1.535851 object centre (A): 53.66350 47.85050 -1.041002 number of atom coordinates read : 5322 total number of charged atoms : 5152 net assigned charge : -0.8999621 assigned positive charge : 817.8515 centred at (gu) : 92.88915 89.37087 91.47236 assigned negative charge : -818.7583 centred at (gu) : 92.75593 89.46986 91.62527 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 94998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 28874 mr = 66303 m= 2638 mr = 20051 m= 45 mr = 1249 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1823 time to turn everything in is 0.7200000 number of dielectric boundary points 38952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 559 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 38696 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) : 0.5119503 object centre at (A) : 53.66350 47.85050 -1.041002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8358310E-03 3.6963697E-03 midg,1,midg; midg,igrid,midg 7.4335090E-03 -1.6384624E-02 1,midg,midg; igrid,midg,midg -5.4083746E-03 1.4680663E-02 gauss-seidel spectral radius is 0.9981518 estimated iterations to convergence 185 setup time was (sec) 1.000000 now iterating at: 15:31:30 rms-change max change #iterations 4.101918 155.6998 at 10iterations 1.705526 53.41187 at 20iterations 0.7062351 22.39853 at 30iterations 0.2933354 9.566628 at 40iterations 0.1221449 3.994701 at 50iterations 5.1182702E-02 1.593307 at 60iterations 2.1814805E-02 0.6703434 at 70iterations 9.6160797E-03 0.2981262 at 80iterations 4.6042120E-03 0.1507950 at 90iterations 2.4784824E-03 8.9749336E-02 at 100iterations 1.4811177E-03 5.4164886E-02 at 110iterations 9.6032006E-04 3.2947540E-02 at 120iterations finished qdiffx linear iterations at : 15:31:37 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 9.6032006E-04 3.2947540E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 15:31:37 7.890u 0.173s 0:08.38 96.1% 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 15:31:37 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 = 5322 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.303777 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): 22.83400 84.49300 ymin,ymax (A): 14.33000 81.37100 zmin,zma (A): -35.81000 33.72800 x,y,z range (A): 61.65900 67.04100 69.53799 scale (grids/A): 2.303777 object centre (A): 53.66350 47.85050 -1.041002 number of atom coordinates read : 5322 total number of charged atoms : 5152 net assigned charge : -0.8999621 assigned positive charge : 817.8515 centred at (gu) : 94.33314 89.05579 92.20804 assigned negative charge : -818.7583 centred at (gu) : 94.13384 89.20473 92.43784 start vw surface at 0.2200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 221305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 101776 mr = 162742 m= 27753 mr = 80941 m= 4031 mr = 20891 m= 191 mr = 2580 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 6379 time to turn everything in is 1.690000 number of dielectric boundary points 87871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 41107 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) : 1.535851 object centre at (A) : 53.66350 47.85050 -1.041002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2042162 0.1595627 midg,1,midg; midg,igrid,midg 0.2011928 -0.3132430 1,midg,midg; igrid,midg,midg -6.9963798E-02 0.4066671 gauss-seidel spectral radius is 0.9991757 estimated iterations to convergence 275 setup time was (sec) 2.010000 now iterating at: 15:31:39 rms-change max change #iterations 11.06638 259.1350 at 10iterations 6.377203 143.1189 at 20iterations 3.639659 82.95354 at 30iterations 2.062607 45.95025 at 40iterations 1.164596 21.57520 at 50iterations 0.6564057 15.86991 at 60iterations 0.3684126 7.419111 at 70iterations 0.2068294 4.103844 at 80iterations 0.1157011 2.379073 at 90iterations 6.4953923E-02 1.167206 at 100iterations 3.6317252E-02 0.6432400 at 110iterations 2.0360153E-02 0.3719482 at 120iterations 1.1448701E-02 0.2078342 at 130iterations 6.4838734E-03 0.1100659 at 140iterations 3.7164050E-03 6.9820404E-02 at 150iterations 2.1720142E-03 3.9737701E-02 at 160iterations 1.3138407E-03 2.6451111E-02 at 170iterations 8.3513197E-04 1.7686844E-02 at 180iterations finished qdiffx linear iterations at : 15:31:50 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.3513197E-04 1.7686844E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 15:31:51 12.874u 0.173s 0:13.31 97.9% 0+0k 0+0io 0pf+0w