Sat Oct 15 14:13:05 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 Sat Oct 15 2011 at 14:13:07 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5050720 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 0.5050720 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4980 net assigned charge : 6.706036 assigned positive charge : 787.8824 centred at (gu) : 90.64393 90.72976 89.44810 assigned negative charge : -781.1816 centred at (gu) : 90.56275 90.75168 89.43532 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8305 nv = 96 ne = 84 npr = 106716 no. pairs analyzed = 106716 no. exposed pairs = 6510 no. arc points = 44661 no. surface atoms = 2210 nbur = 3026 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 = 1.680000 m= 310 mr = 4310 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4403 ## 721 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1486412E-11 8.8242018E-11 midg,1,midg; midg,igrid,midg 1.0093820E-10 2.8870741E-11 1,midg,midg; igrid,midg,midg -9.1896532E-11 3.0029676E-10 gauss-seidel spectral radius is 0.9799831 estimated iterations to convergence 58 setup time was (sec) 0.5400000 now iterating at: 14:13:09 rms-change max change #iterations 6.8970732E-02 10.70216 at 10iterations 4.6345592E-03 0.7096214 at 20iterations 8.6287013E-04 0.1144791 at 30iterations 3.1175802E-04 3.6376953E-02 at 40iterations 1.2312802E-04 1.5764236E-02 at 50iterations finished qdiffx linear iterations at : 14:13:15 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.2312802E-04 1.5764236E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 14:13:16 3.783u 0.226s 0:09.52 42.0% 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 Sat Oct 15 2011 at 14:13:16 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.515216 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 1.515216 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4980 net assigned charge : 6.706036 assigned positive charge : 787.8824 centred at (gu) : 91.93031 92.18771 88.34266 assigned negative charge : -781.1816 centred at (gu) : 91.68795 92.25485 88.30542 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 95385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 26858 mr = 66059 m= 2415 mr = 17476 m= 67 mr = 972 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 40216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 653 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 37335 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) : 0.5050720 object centre at (A) : 8.838501 0.9064999 31.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7335337E-03 1.6560566E-02 midg,1,midg; midg,igrid,midg -1.5780444E-03 -1.0781375E-02 1,midg,midg; igrid,midg,midg -1.0876029E-03 1.0564269E-02 gauss-seidel spectral radius is 0.9981043 estimated iterations to convergence 183 setup time was (sec) 0.7400000 now iterating at: 14:13:17 rms-change max change #iterations 3.917190 157.9594 at 10iterations 1.599764 53.01431 at 20iterations 0.6549977 20.69738 at 30iterations 0.2691329 8.816983 at 40iterations 0.1101812 3.595488 at 50iterations 4.5351222E-02 1.378121 at 60iterations 1.8609533E-02 0.5887489 at 70iterations 7.6933256E-03 0.2395105 at 80iterations 3.2557477E-03 0.1005344 at 90iterations 1.4302821E-03 4.4586182E-02 at 100iterations 6.9956528E-04 2.4055481E-02 at 110iterations 3.9203532E-04 1.1949539E-02 at 120iterations finished qdiffx linear iterations at : 14:13:33 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 3.9203532E-04 1.1949539E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 14:13:33 8.626u 0.261s 0:17.43 50.9% 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 Sat Oct 15 2011 at 14:13:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.272824 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 2.272824 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4980 net assigned charge : 6.706036 assigned positive charge : 787.8824 centred at (gu) : 92.89501 93.28130 87.51367 assigned negative charge : -781.1816 centred at (gu) : 92.53172 93.38210 87.45807 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 222976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 97031 mr = 162867 m= 23605 mr = 75022 m= 3392 mr = 16448 m= 178 mr = 2010 m= 0 mr = 54 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 90781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 39712 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) : 1.515216 object centre at (A) : 8.838501 0.9064999 31.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1232170 0.3123079 midg,1,midg; midg,igrid,midg -0.1133797 -0.2568014 1,midg,midg; igrid,midg,midg -1.3181400E-02 0.1680445 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.400000 now iterating at: 14:13:38 rms-change max change #iterations 10.63742 349.6716 at 10iterations 6.118538 133.5572 at 20iterations 3.484523 90.67133 at 30iterations 1.973846 41.87245 at 40iterations 1.114279 28.68623 at 50iterations 0.6264392 13.14118 at 60iterations 0.3528642 7.875759 at 70iterations 0.1975999 3.744301 at 80iterations 0.1106542 2.111103 at 90iterations 6.1822399E-02 1.201649 at 100iterations 3.4609009E-02 0.6760483 at 110iterations 1.9279838E-02 0.3638077 at 120iterations 1.0771487E-02 0.1982956 at 130iterations 6.0250964E-03 0.1257834 at 140iterations 3.3664661E-03 6.5628052E-02 at 150iterations 1.8885327E-03 3.9275169E-02 at 160iterations 1.0670334E-03 2.2449493E-02 at 170iterations 6.1099016E-04 1.1672020E-02 at 180iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 14.66000 # loops : 180 mean,max change (kT/e) : 6.1099016E-04 1.1672020E-02 energy calculations done at 14.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.80000 DelPhi exited at 14:14:05 14.803u 0.260s 0:31.09 48.4% 0+0k 0+0io 0pf+0w