Tue Oct 11 06:15:40 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+sph.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 = amb.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 06:15:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 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: 0.6839051 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 0.6839051 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1981 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 91.52084 89.64825 89.23170 assigned negative charge : -314.6841 centred at (gu) : 91.64460 89.67747 89.15496 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6635 nv = 96 ne = 84 npr = 42233 no. pairs analyzed = 42233 no. exposed pairs = 2561 no. arc points = 17434 no. surface atoms = 870 nbur = 1239 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3797 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1711 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0499318E-08 4.6003368E-08 midg,1,midg; midg,igrid,midg 4.2856595E-08 2.1624206E-08 1,midg,midg; igrid,midg,midg 4.9447067E-08 -7.1181074E-09 gauss-seidel spectral radius is 0.9888641 estimated iterations to convergence 77 setup time was (sec) 0.5800000 now iterating at: 06:15:41 rms-change max change #iterations 0.1758379 27.42056 at 10iterations 2.0329311E-02 2.702606 at 20iterations 2.5676216E-03 0.3784981 at 30iterations 4.1167249E-04 6.4109802E-02 at 40iterations 1.0766164E-04 1.5695572E-02 at 50iterations finished qdiffx linear iterations at : 06:15:44 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.0766164E-04 1.5695572E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 06:15:45 4.028u 0.248s 0:04.65 91.6% 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 Tue Oct 11 2011 at 06:15:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.051715 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 2.051715 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1981 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 94.56256 88.94482 87.69502 assigned negative charge : -314.6841 centred at (gu) : 94.93373 89.03257 87.46493 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 27901 mr = 50453 m= 4902 mr = 20965 m= 387 mr = 3196 m= 7 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 29332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15679 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) : 0.6839051 object centre at (A) : 39.17950 15.10200 45.96400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7342454E-02 4.7065016E-02 midg,1,midg; midg,igrid,midg 2.3488304E-02 9.6428366E-03 1,midg,midg; igrid,midg,midg 2.2388270E-02 1.4715035E-02 gauss-seidel spectral radius is 0.9987602 estimated iterations to convergence 225 setup time was (sec) 0.9300000 now iterating at: 06:15:46 rms-change max change #iterations 4.350149 205.4697 at 10iterations 2.117583 78.64957 at 20iterations 1.024731 37.78239 at 30iterations 0.4989750 14.82658 at 40iterations 0.2437999 7.351170 at 50iterations 0.1182045 3.577492 at 60iterations 5.7693299E-02 1.798818 at 70iterations 2.8169125E-02 0.8969669 at 80iterations 1.3742539E-02 0.4389858 at 90iterations 6.7272787E-03 0.1957245 at 100iterations 3.3367418E-03 0.1199694 at 110iterations 1.6842606E-03 5.6435585E-02 at 120iterations finished qdiffx linear iterations at : 06:15:54 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 1.6842606E-03 5.6435585E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 06:15:55 9.321u 0.316s 0:10.03 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 Tue Oct 11 2011 at 06:15:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 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: 3.077573 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 3.077573 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1981 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 96.84364 88.41719 86.54250 assigned negative charge : -314.6841 centred at (gu) : 97.40052 88.54877 86.19742 start vw surface at 0.1400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 163482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 88113 mr = 121204 m= 34274 mr = 73237 m= 9072 mr = 27929 m= 1667 mr = 6981 m= 166 mr = 1234 m= 6 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 66100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15843 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) : 2.051715 object centre at (A) : 39.17950 15.10200 45.96400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2434816 0.3578417 midg,1,midg; midg,igrid,midg 0.2183817 6.8866760E-02 1,midg,midg; igrid,midg,midg 0.1967076 0.3789333 gauss-seidel spectral radius is 0.9992801 estimated iterations to convergence 294 setup time was (sec) 2.370000 now iterating at: 06:15:57 rms-change max change #iterations 9.887395 389.5919 at 10iterations 5.808897 122.2615 at 20iterations 3.411469 70.85192 at 30iterations 2.004076 41.80788 at 40iterations 1.174227 24.13529 at 50iterations 0.6851050 14.13776 at 60iterations 0.4000022 7.635878 at 70iterations 0.2329475 4.253801 at 80iterations 0.1360913 2.608854 at 90iterations 7.9177856E-02 1.560917 at 100iterations 4.6216413E-02 0.8672409 at 110iterations 2.6975546E-02 0.5105209 at 120iterations 1.5826579E-02 0.2849607 at 130iterations 9.3627004E-03 0.1795073 at 140iterations 5.6178188E-03 0.1028194 at 150iterations 3.4641721E-03 6.3916743E-02 at 160iterations 2.2323092E-03 4.3369293E-02 at 170iterations 1.5195337E-03 3.0492783E-02 at 180iterations finished qdiffx linear iterations at : 06:16:11 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 1.5195337E-03 3.0492783E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.99000 DelPhi exited at 06:16:11 15.992u 0.331s 0:16.79 97.2% 0+0k 0+0io 0pf+0w