Mon Oct 10 09:17:27 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 09:17:27 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5941156 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 0.5941156 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.05514 89.47782 89.62861 assigned negative charge : -290.0002 centred at (gu) : 89.97202 89.62446 89.63828 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4668 nv = 96 ne = 84 npr = 40200 no. pairs analyzed = 40200 no. exposed pairs = 2505 no. arc points = 17539 no. surface atoms = 856 nbur = 1114 mkacc time = 7.0000008E-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 = 1.456000 m= 205 mr = 2464 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5695 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3695953E-09 7.5778411E-10 midg,1,midg; midg,igrid,midg 4.8656874E-09 -2.0699458E-09 1,midg,midg; igrid,midg,midg -8.5162599E-10 2.9461575E-09 gauss-seidel spectral radius is 0.9852869 estimated iterations to convergence 68 setup time was (sec) 0.3500000 now iterating at: 09:17:28 rms-change max change #iterations 8.9257844E-02 16.51301 at 10iterations 7.4800863E-03 1.388399 at 20iterations 6.2363711E-04 0.1177254 at 30iterations 4.9626313E-05 8.5525513E-03 at 40iterations 4.1942976E-06 7.0571899E-04 at 50iterations finished qdiffx linear iterations at : 09:17:31 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.1942976E-06 7.0571899E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 09:17:31 3.341u 0.168s 0:03.86 90.6% 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 09:17:31 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.782347 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 1.782347 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.16547 88.43363 88.88557 assigned negative charge : -290.0002 centred at (gu) : 89.91613 88.87375 88.91489 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 50307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17539 grid for indexing accessible points = 1.400000 m= 17314 mr = 33932 m= 2204 mr = 12771 m= 86 mr = 1327 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 0.2600000 number of dielectric boundary points 21861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 14288 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) : 0.5941156 object centre at (A) : -11.88400 21.31900 28.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5858376E-02 2.0775739E-02 midg,1,midg; midg,igrid,midg 3.7358280E-03 -6.6336216E-03 1,midg,midg; igrid,midg,midg -1.6470274E-03 -4.8477086E-04 gauss-seidel spectral radius is 0.9983668 estimated iterations to convergence 196 setup time was (sec) 0.4700000 now iterating at: 09:17:32 rms-change max change #iterations 3.183876 181.3287 at 10iterations 1.388225 54.74940 at 20iterations 0.6062120 23.54801 at 30iterations 0.2631452 10.08653 at 40iterations 0.1146373 4.837082 at 50iterations 5.0254405E-02 1.967188 at 60iterations 2.1788685E-02 0.8056717 at 70iterations 9.4829369E-03 0.3722095 at 80iterations 4.1179084E-03 0.1529961 at 90iterations 1.8036694E-03 6.9744110E-02 at 100iterations 7.8439625E-04 2.9019356E-02 at 110iterations 3.4379249E-04 1.4456630E-02 at 120iterations finished qdiffx linear iterations at : 09:17:39 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 3.4379249E-04 1.4456630E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 09:17:39 7.555u 0.197s 0:08.11 95.4% 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 Mon Oct 10 2011 at 09:17:39 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.673520 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 2.673520 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.24811 87.65046 88.32844 assigned negative charge : -290.0002 centred at (gu) : 89.87431 88.31068 88.37233 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 116205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17539 grid for indexing accessible points = 1.400000 m= 57055 mr = 82426 m= 19419 mr = 46400 m= 3817 mr = 15684 m= 382 mr = 2856 m= 13 mr = 220 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1150 time to turn everything in is 0.6300000 number of dielectric boundary points 49302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14701 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) : 1.782347 object centre at (A) : -11.88400 21.31900 28.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2089301 0.1170177 midg,1,midg; midg,igrid,midg -5.7756359E-04 -9.9290408E-02 1,midg,midg; igrid,midg,midg -4.1895621E-02 -3.1643454E-02 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 0.8500000 now iterating at: 09:17:40 rms-change max change #iterations 7.707105 278.2611 at 10iterations 4.299273 154.0392 at 20iterations 2.402289 62.13522 at 30iterations 1.329751 29.82502 at 40iterations 0.7366123 15.56546 at 50iterations 0.4074766 9.518112 at 60iterations 0.2252415 4.756989 at 70iterations 0.1246553 2.747591 at 80iterations 6.8905443E-02 1.540257 at 90iterations 3.8215321E-02 0.9379578 at 100iterations 2.1135783E-02 0.4594193 at 110iterations 1.1682466E-02 0.2780137 at 120iterations 6.4452370E-03 0.1594906 at 130iterations 3.5619247E-03 7.8876019E-02 at 140iterations 1.9705994E-03 4.8593044E-02 at 150iterations 1.0937250E-03 2.2313118E-02 at 160iterations 6.0279825E-04 1.2649536E-02 at 170iterations 3.3297422E-04 7.3041916E-03 at 180iterations finished qdiffx linear iterations at : 09:17:51 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 3.3297422E-04 7.3041916E-03 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 09:17:53 11.798u 0.207s 0:13.22 90.6% 0+0k 0+0io 0pf+0w