Sun Oct 9 08:19:36 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 08:19:36 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 !!! WARNING: HIR 700 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.4804772 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 0.4804772 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.514045 assigned positive charge : 910.9380 centred at (gu) : 90.42662 90.68309 90.37515 assigned negative charge : -908.4317 centred at (gu) : 90.39591 90.77145 90.28750 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8433 nv = 96 ne = 84 npr = 122308 no. pairs analyzed = 122308 no. exposed pairs = 7617 no. arc points = 52087 no. surface atoms = 2555 nbur = 3473 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 = 1.764000 m= 266 mr = 4208 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5400000 number of dielectric boundary points 4488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4871 ## 835 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9133323E-11 9.0562662E-11 midg,1,midg; midg,igrid,midg 6.7733659E-11 -8.0702618E-11 1,midg,midg; igrid,midg,midg -1.5166181E-11 3.8814230E-11 gauss-seidel spectral radius is 0.9779443 estimated iterations to convergence 56 setup time was (sec) 0.7600000 now iterating at: 08:19:37 rms-change max change #iterations 5.6857843E-02 9.393480 at 10iterations 3.1169839E-03 0.5245438 at 20iterations 4.1731147E-04 9.3708038E-02 at 30iterations 1.1327596E-04 2.4158478E-02 at 40iterations 3.3942593E-05 6.7481995E-03 at 50iterations finished qdiffx linear iterations at : 08:19:39 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.3942593E-05 6.7481995E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:19:40 3.397u 0.145s 0:03.82 92.4% 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 08:19:40 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 !!! WARNING: HIR 700 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: 1.441432 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 1.441432 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.514045 assigned positive charge : 910.9380 centred at (gu) : 91.27831 92.04731 91.12331 assigned negative charge : -908.4317 centred at (gu) : 91.18745 92.31385 90.86205 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 95878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52087 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25465 mr = 64388 m= 1791 mr = 16115 m= 22 mr = 578 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 0.6700000 number of dielectric boundary points 42075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 858 ## 21 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 42999 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) : 0.4804772 object centre at (A) : 109.9680 -79.76300 -50.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3402704E-03 9.1953231E-03 midg,1,midg; midg,igrid,midg 5.2494127E-03 -1.2486222E-03 1,midg,midg; igrid,midg,midg -7.2630015E-03 7.3676661E-04 gauss-seidel spectral radius is 0.9979454 estimated iterations to convergence 175 setup time was (sec) 0.9500000 now iterating at: 08:19:41 rms-change max change #iterations 3.749969 145.1354 at 10iterations 1.474173 53.64164 at 20iterations 0.5833463 21.11807 at 30iterations 0.2301098 7.668304 at 40iterations 9.0974733E-02 3.043712 at 50iterations 3.5993274E-02 1.104118 at 60iterations 1.4281566E-02 0.4608960 at 70iterations 5.6713778E-03 0.1785126 at 80iterations 2.2790409E-03 7.3394775E-02 at 90iterations 9.3974243E-04 3.1471252E-02 at 100iterations 4.0475273E-04 1.5235901E-02 at 110iterations 1.8987528E-04 7.0037842E-03 at 120iterations finished qdiffx linear iterations at : 08:19:47 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 1.8987528E-04 7.0037842E-03 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 08:19:47 7.287u 0.177s 0:07.76 96.0% 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 08:19:47 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 !!! WARNING: HIR 700 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.162148 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 2.162148 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.514045 assigned positive charge : 910.9380 centred at (gu) : 91.91710 93.07050 91.68456 assigned negative charge : -908.4317 centred at (gu) : 91.78122 93.47082 91.29308 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 224056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52087 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 94055 mr = 159452 m= 21007 mr = 71542 m= 2207 mr = 14256 m= 58 mr = 1103 m= 0 mr = 8 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 2971 time to turn everything in is 1.560000 number of dielectric boundary points 95022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 46641 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) : 1.441432 object centre at (A) : 109.9680 -79.76300 -50.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2544138 1.5080014E-02 midg,1,midg; midg,igrid,midg 9.2303008E-02 -9.6892677E-03 1,midg,midg; igrid,midg,midg -0.1930924 8.4328810E-03 gauss-seidel spectral radius is 0.9991402 estimated iterations to convergence 269 setup time was (sec) 1.860000 now iterating at: 08:19:49 rms-change max change #iterations 10.66220 348.3027 at 10iterations 6.078402 153.8437 at 20iterations 3.447557 83.01576 at 30iterations 1.944228 47.13780 at 40iterations 1.095005 30.52982 at 50iterations 0.6124104 11.79546 at 60iterations 0.3428538 7.061243 at 70iterations 0.1912721 3.730268 at 80iterations 0.1064582 2.200577 at 90iterations 5.9217490E-02 1.102188 at 100iterations 3.2929391E-02 0.6220169 at 110iterations 1.8284095E-02 0.3624573 at 120iterations 1.0148644E-02 0.1975975 at 130iterations 5.6338590E-03 0.1073320 at 140iterations 3.1379161E-03 6.1075211E-02 at 150iterations 1.7468805E-03 3.2128334E-02 at 160iterations 9.7680255E-04 1.8386841E-02 at 170iterations 5.5147544E-04 1.0306358E-02 at 180iterations finished qdiffx linear iterations at : 08:19:59 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 5.5147544E-04 1.0306358E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 08:20:00 11.925u 0.212s 0:12.39 97.9% 0+0k 0+0io 0pf+0w