Tue Oct 11 08:40:25 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+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 Tue Oct 11 2011 at 08:40:26 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2450 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5827658 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): -6.835000 54.25300 ymin,ymax (A): -22.76600 25.46300 zmin,zma (A): 9.211000 54.73100 x,y,z range (A): 61.08800 48.22900 45.52000 scale (grids/A): 0.5827658 object centre (A): 23.70900 1.348499 31.97100 number of atom coordinates read : 2450 total number of charged atoms : 2300 net assigned charge : 7.486016 assigned positive charge : 374.1543 centred at (gu) : 89.86645 89.43347 89.86340 assigned negative charge : -366.6687 centred at (gu) : 89.91925 89.39180 89.68947 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5466 nv = 96 ne = 84 npr = 48545 no. pairs analyzed = 48545 no. exposed pairs = 3000 no. arc points = 21318 no. surface atoms = 1017 nbur = 1433 mkacc time = 7.9999998E-02 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 = 1.484000 m= 272 mr = 2897 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 311 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7805328E-09 5.0416005E-09 midg,1,midg; midg,igrid,midg 1.1078893E-09 2.3181936E-09 1,midg,midg; igrid,midg,midg 2.9470775E-09 7.3521739E-10 gauss-seidel spectral radius is 0.9847565 estimated iterations to convergence 67 setup time was (sec) 0.3600000 now iterating at: 08:40:26 rms-change max change #iterations 9.5739618E-02 17.00317 at 10iterations 8.2825897E-03 1.395187 at 20iterations 1.0663203E-03 0.1771317 at 30iterations 2.1722757E-04 3.6317825E-02 at 40iterations 4.9465827E-05 8.3866119E-03 at 50iterations finished qdiffx linear iterations at : 08:40:29 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.9465827E-05 8.3866119E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:40:29 3.327u 0.166s 0:03.79 91.8% 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 Tue Oct 11 2011 at 08:40:29 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2450 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.748297 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): -6.835000 54.25300 ymin,ymax (A): -22.76600 25.46300 zmin,zma (A): 9.211000 54.73100 x,y,z range (A): 61.08800 48.22900 45.52000 scale (grids/A): 1.748297 object centre (A): 23.70900 1.348499 31.97100 number of atom coordinates read : 2450 total number of charged atoms : 2300 net assigned charge : 7.486016 assigned positive charge : 374.1543 centred at (gu) : 89.59899 88.30008 89.58993 assigned negative charge : -366.6687 centred at (gu) : 89.75772 88.17528 89.06805 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21318 grid for indexing accessible points = 1.400000 m= 20478 mr = 41294 m= 2322 mr = 14717 m= 81 mr = 1178 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 25938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 17891 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) : 0.5827658 object centre at (A) : 23.70900 1.348499 31.97100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6690198E-03 2.1636248E-02 midg,1,midg; midg,igrid,midg 1.2186184E-03 3.7748022E-03 1,midg,midg; igrid,midg,midg 1.5141590E-02 2.3894193E-02 gauss-seidel spectral radius is 0.9983700 estimated iterations to convergence 197 setup time was (sec) 0.5100000 now iterating at: 08:40:30 rms-change max change #iterations 3.471918 180.1341 at 10iterations 1.506576 66.78257 at 20iterations 0.6583801 29.21915 at 30iterations 0.2898971 11.78368 at 40iterations 0.1261936 4.613924 at 50iterations 5.5671073E-02 1.943474 at 60iterations 2.4571935E-02 0.9600143 at 70iterations 1.0991171E-02 0.3711662 at 80iterations 4.9472237E-03 0.1954269 at 90iterations 2.2904028E-03 8.4846497E-02 at 100iterations 1.1129706E-03 4.4460297E-02 at 110iterations 5.6440453E-04 2.2087097E-02 at 120iterations finished qdiffx linear iterations at : 08:40:37 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 5.6440453E-04 2.2087097E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 08:40:37 7.533u 0.182s 0:08.07 95.5% 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 Tue Oct 11 2011 at 08:40:37 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2450 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.622446 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): -6.835000 54.25300 ymin,ymax (A): -22.76600 25.46300 zmin,zma (A): 9.211000 54.73100 x,y,z range (A): 61.08800 48.22900 45.52000 scale (grids/A): 2.622446 object centre (A): 23.70900 1.348499 31.97100 number of atom coordinates read : 2450 total number of charged atoms : 2300 net assigned charge : 7.486016 assigned positive charge : 374.1543 centred at (gu) : 89.39858 87.44996 89.38483 assigned negative charge : -366.6687 centred at (gu) : 89.63656 87.26295 88.60212 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 139356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21318 grid for indexing accessible points = 1.400000 m= 68476 mr = 99937 m= 21759 mr = 55734 m= 3719 mr = 16861 m= 334 mr = 2458 m= 12 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 58489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18390 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) : 1.748297 object centre at (A) : 23.70900 1.348499 31.97100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1679921 0.2664842 midg,1,midg; midg,igrid,midg -9.3400581E-03 -5.5110301E-03 1,midg,midg; igrid,midg,midg -4.2243827E-02 0.2455225 gauss-seidel spectral radius is 0.9991778 estimated iterations to convergence 275 setup time was (sec) 0.9700000 now iterating at: 08:40:39 rms-change max change #iterations 8.515972 265.6051 at 10iterations 4.820866 115.7885 at 20iterations 2.706896 61.12547 at 30iterations 1.515314 37.08004 at 40iterations 0.8467050 16.96930 at 50iterations 0.4740749 9.769348 at 60iterations 0.2650492 6.651152 at 70iterations 0.1478781 2.974251 at 80iterations 8.2621694E-02 1.668045 at 90iterations 4.6109334E-02 1.058725 at 100iterations 2.5781350E-02 0.5348473 at 110iterations 1.4397010E-02 0.2901048 at 120iterations 8.0725364E-03 0.1688251 at 130iterations 4.5330329E-03 0.1058297 at 140iterations 2.5689981E-03 5.3634644E-02 at 150iterations 1.4766596E-03 3.3020020E-02 at 160iterations 8.6494425E-04 1.9119263E-02 at 170iterations 5.2211829E-04 1.3847351E-02 at 180iterations finished qdiffx linear iterations at : 08:40:49 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 5.2211829E-04 1.3847351E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 08:40:50 11.959u 0.197s 0:12.65 95.9% 0+0k 0+0io 0pf+0w