Mon Oct 10 17:05:52 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 17:05:52 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2503 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5560588 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 0.5560588 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2362 net assigned charge : 6.906023 assigned positive charge : 369.3239 centred at (gu) : 90.33429 88.96171 89.44628 assigned negative charge : -362.4188 centred at (gu) : 90.37585 88.87394 89.56709 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5067 nv = 96 ne = 84 npr = 50345 no. pairs analyzed = 50345 no. exposed pairs = 3211 no. arc points = 23133 no. surface atoms = 1077 nbur = 1426 mkacc time = 0.1300000 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= 199 mr = 2551 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7964834E-09 -2.7867686E-10 midg,1,midg; midg,igrid,midg -8.5405523E-11 1.0263004E-09 1,midg,midg; igrid,midg,midg 8.8721641E-10 3.3390718E-10 gauss-seidel spectral radius is 0.9832848 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 17:05:53 rms-change max change #iterations 7.4813880E-02 13.78320 at 10iterations 5.1560421E-03 0.8977661 at 20iterations 3.5866510E-04 6.0182571E-02 at 30iterations 2.5695861E-05 4.9133301E-03 at 40iterations 1.8237563E-06 3.4523010E-04 at 50iterations finished qdiffx linear iterations at : 17:05:57 total time elapsed so far: 5.030000 # loops : 50 mean,max change (kT/e) : 1.8237563E-06 3.4523010E-04 energy calculations done at 5.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.210000 DelPhi exited at 17:05:58 5.211u 0.455s 0:06.07 93.2% 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 Mon Oct 10 2011 at 17:05:58 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 = 2503 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.668177 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 1.668177 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2362 net assigned charge : 6.906023 assigned positive charge : 369.3239 centred at (gu) : 91.00233 86.88441 88.33808 assigned negative charge : -362.4188 centred at (gu) : 91.12759 86.62183 88.70117 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 56074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23133 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17251 mr = 37277 m= 1866 mr = 11779 m= 60 mr = 905 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 253 time to turn everything in is 0.4900000 number of dielectric boundary points 25287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18184 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) : 0.5560588 object centre at (A) : 17.07700 16.28200 30.52700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2828428E-02 1.2791447E-02 midg,1,midg; midg,igrid,midg -9.3047041E-03 5.9713866E-03 1,midg,midg; igrid,midg,midg 7.4609863E-03 1.7017513E-03 gauss-seidel spectral radius is 0.9982094 estimated iterations to convergence 188 setup time was (sec) 0.8200000 now iterating at: 17:05:59 rms-change max change #iterations 3.115631 135.8250 at 10iterations 1.306247 54.56592 at 20iterations 0.5447795 20.59912 at 30iterations 0.2280833 8.605848 at 40iterations 9.5819391E-02 3.645983 at 50iterations 4.0152900E-02 1.534145 at 60iterations 1.6865028E-02 0.6348209 at 70iterations 7.0539652E-03 0.2965803 at 80iterations 2.9433782E-03 0.1107826 at 90iterations 1.2335791E-03 4.9507141E-02 at 100iterations 5.1873300E-04 1.7864227E-02 at 110iterations 2.1727268E-04 8.6610317E-03 at 120iterations finished qdiffx linear iterations at : 17:06:10 total time elapsed so far: 11.45000 # loops : 120 mean,max change (kT/e) : 2.1727268E-04 8.6610317E-03 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 17:06:11 11.629u 0.517s 0:12.86 94.3% 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 17:06:11 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 = 2503 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.502265 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 2.502265 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2362 net assigned charge : 6.906023 assigned positive charge : 369.3239 centred at (gu) : 91.50330 85.32650 87.50691 assigned negative charge : -362.4188 centred at (gu) : 91.69142 84.93268 88.05168 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 130281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23133 grid for indexing accessible points = 1.400000 m= 59627 mr = 91433 m= 17095 mr = 46862 m= 2907 mr = 12734 m= 237 mr = 1910 m= 7 mr = 112 m= 0 mr = 2 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 784 time to turn everything in is 1.170000 number of dielectric boundary points 57101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 18876 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) : 1.668177 object centre at (A) : 17.07700 16.28200 30.52700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2801091 0.2591344 midg,1,midg; midg,igrid,midg -9.6759237E-02 0.1334637 1,midg,midg; igrid,midg,midg 9.1075219E-02 8.8781239E-03 gauss-seidel spectral radius is 0.9991346 estimated iterations to convergence 269 setup time was (sec) 1.540000 now iterating at: 17:06:13 rms-change max change #iterations 7.977833 251.6010 at 10iterations 4.468812 131.5059 at 20iterations 2.479476 63.28027 at 30iterations 1.372282 33.47815 at 40iterations 0.7564009 17.57731 at 50iterations 0.4173233 9.816256 at 60iterations 0.2299203 5.537888 at 70iterations 0.1262444 2.679931 at 80iterations 6.9199152E-02 1.555645 at 90iterations 3.8063392E-02 0.8020849 at 100iterations 2.0839253E-02 0.4540348 at 110iterations 1.1433351E-02 0.2448502 at 120iterations 6.2689297E-03 0.1373138 at 130iterations 3.4320010E-03 7.6951981E-02 at 140iterations 1.8812262E-03 3.9937973E-02 at 150iterations 1.0312885E-03 2.1595001E-02 at 160iterations 5.6484481E-04 1.4350891E-02 at 170iterations 3.0974299E-04 6.5841675E-03 at 180iterations finished qdiffx linear iterations at : 17:06:31 total time elapsed so far: 19.62000 # loops : 180 mean,max change (kT/e) : 3.0974299E-04 6.5841675E-03 energy calculations done at 19.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.78000 DelPhi exited at 17:06:32 19.788u 0.523s 0:20.95 96.8% 0+0k 0+0io 0pf+0w