Mon Oct 10 17:00:38 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 Mon Oct 10 2011 at 17:00:38 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4440 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5117884 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): -16.45500 37.29900 ymin,ymax (A): -32.96100 32.35900 zmin,zma (A): -4.022000 65.53800 x,y,z range (A): 53.75400 65.32000 69.56001 scale (grids/A): 0.5117884 object centre (A): 10.42200 -0.3009987 30.75800 number of atom coordinates read : 4440 total number of charged atoms : 4196 net assigned charge : 3.700025 assigned positive charge : 659.5890 centred at (gu) : 90.14594 90.93896 87.50842 assigned negative charge : -655.8931 centred at (gu) : 90.00531 90.97532 87.52937 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7418 nv = 96 ne = 84 npr = 90142 no. pairs analyzed = 90142 no. exposed pairs = 5759 no. arc points = 39698 no. surface atoms = 1920 nbur = 2520 mkacc time = 0.1500000 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 = 1.652000 m= 272 mr = 3804 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3765 ## 560 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0493529E-10 1.7866604E-12 midg,1,midg; midg,igrid,midg 1.1259047E-10 -4.8015748E-11 1,midg,midg; igrid,midg,midg -2.9016511E-10 4.1238871E-10 gauss-seidel spectral radius is 0.9804530 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 17:00:39 rms-change max change #iterations 6.7077987E-02 10.54409 at 10iterations 3.9424486E-03 0.5703678 at 20iterations 4.5246136E-04 6.9610596E-02 at 30iterations 1.4564740E-04 1.9760728E-02 at 40iterations 5.3714910E-05 8.0094934E-03 at 50iterations finished qdiffx linear iterations at : 17:00:42 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.3714910E-05 8.0094934E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 17:00:42 3.569u 0.167s 0:04.27 87.1% 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 17:00:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4440 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.535365 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): -16.45500 37.29900 ymin,ymax (A): -32.96100 32.35900 zmin,zma (A): -4.022000 65.53800 x,y,z range (A): 53.75400 65.32000 69.56001 scale (grids/A): 1.535365 object centre (A): 10.42200 -0.3009987 30.75800 number of atom coordinates read : 4440 total number of charged atoms : 4196 net assigned charge : 3.700025 assigned positive charge : 659.5890 centred at (gu) : 90.43623 92.81554 82.52412 assigned negative charge : -655.8931 centred at (gu) : 90.01575 92.92552 82.58789 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 84094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39698 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23781 mr = 57316 m= 2019 mr = 15462 m= 38 mr = 786 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.4100000 number of dielectric boundary points 36364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 532 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31560 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) : 0.5117884 object centre at (A) : 10.42200 -0.3009987 30.75800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9038109E-03 8.5795941E-03 midg,1,midg; midg,igrid,midg -9.2846848E-04 -9.8577468E-03 1,midg,midg; igrid,midg,midg -4.8701982E-03 9.5009282E-03 gauss-seidel spectral radius is 0.9980910 estimated iterations to convergence 182 setup time was (sec) 0.6300000 now iterating at: 17:00:43 rms-change max change #iterations 3.646688 137.7188 at 10iterations 1.482955 51.65736 at 20iterations 0.6054203 22.14443 at 30iterations 0.2460652 8.653088 at 40iterations 0.1005028 3.491297 at 50iterations 4.1197371E-02 1.348562 at 60iterations 1.6778680E-02 0.5572357 at 70iterations 6.8838638E-03 0.2128401 at 80iterations 2.8489761E-03 0.1013975 at 90iterations 1.1962218E-03 3.7509918E-02 at 100iterations 5.2692468E-04 1.9483566E-02 at 110iterations 2.5178312E-04 1.0587215E-02 at 120iterations finished qdiffx linear iterations at : 17:00:51 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 2.5178312E-04 1.0587215E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 17:00:51 8.244u 0.219s 0:09.00 93.8% 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 Mon Oct 10 2011 at 17:00:52 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4440 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.303048 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): -16.45500 37.29900 ymin,ymax (A): -32.96100 32.35900 zmin,zma (A): -4.022000 65.53800 x,y,z range (A): 53.75400 65.32000 69.56001 scale (grids/A): 2.303048 object centre (A): 10.42200 -0.3009987 30.75800 number of atom coordinates read : 4440 total number of charged atoms : 4196 net assigned charge : 3.700025 assigned positive charge : 659.5890 centred at (gu) : 90.65413 94.22304 78.78571 assigned negative charge : -655.8931 centred at (gu) : 90.02342 94.38828 78.88167 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39698 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85985 mr = 140945 m= 20844 mr = 66337 m= 2795 mr = 14657 m= 141 mr = 1637 m= 0 mr = 37 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 836 time to turn everything in is 0.9900000 number of dielectric boundary points 82021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 33485 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) : 1.535365 object centre at (A) : 10.42200 -0.3009987 30.75800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1729071 0.2613202 midg,1,midg; midg,igrid,midg -5.4777887E-02 -0.3060630 1,midg,midg; igrid,midg,midg -5.0019402E-02 0.1344928 gauss-seidel spectral radius is 0.9991505 estimated iterations to convergence 271 setup time was (sec) 1.250000 now iterating at: 17:00:53 rms-change max change #iterations 9.842159 305.5451 at 10iterations 5.609117 125.0236 at 20iterations 3.173982 66.13374 at 30iterations 1.789842 42.65315 at 40iterations 1.004203 22.09433 at 50iterations 0.5616196 11.34224 at 60iterations 0.3131269 7.581526 at 70iterations 0.1742649 3.923100 at 80iterations 9.7097635E-02 2.073662 at 90iterations 5.3951647E-02 1.146107 at 100iterations 2.9989609E-02 0.6403637 at 110iterations 1.6592540E-02 0.3617579 at 120iterations 9.2127537E-03 0.1709518 at 130iterations 5.0983895E-03 9.9029541E-02 at 140iterations 2.8255426E-03 5.6141853E-02 at 150iterations 1.5695976E-03 3.2701492E-02 at 160iterations 8.7005395E-04 1.7630577E-02 at 170iterations 4.8439854E-04 1.0673523E-02 at 180iterations finished qdiffx linear iterations at : 17:01:05 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 4.8439854E-04 1.0673523E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 17:01:05 13.025u 0.208s 0:13.63 96.9% 0+0k 0+0io 0pf+0w