Mon Oct 10 17:04:30 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 17:04:30 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 = 3734 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5528809 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 0.5528809 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3539 net assigned charge : 5.300022 assigned positive charge : 561.4838 centred at (gu) : 90.80154 90.81557 90.97410 assigned negative charge : -556.1855 centred at (gu) : 90.92863 90.86032 90.95092 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7306 nv = 96 ne = 84 npr = 75485 no. pairs analyzed = 75485 no. exposed pairs = 4881 no. arc points = 33856 no. surface atoms = 1626 nbur = 2108 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 = 1.568000 m= 303 mr = 3742 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3406 ## 408 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9609 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5797263E-10 8.7720126E-10 midg,1,midg; midg,igrid,midg 7.5595435E-10 -5.0017070E-11 1,midg,midg; igrid,midg,midg 1.4658419E-09 -1.1502441E-09 gauss-seidel spectral radius is 0.9831875 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 17:04:31 rms-change max change #iterations 8.9820936E-02 15.70644 at 10iterations 6.6135982E-03 0.9215546 at 20iterations 1.0236773E-03 0.1730118 at 30iterations 3.2142748E-04 5.5189133E-02 at 40iterations 1.1241064E-04 1.9321442E-02 at 50iterations finished qdiffx linear iterations at : 17:04:34 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.1241064E-04 1.9321442E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 17:04:34 3.674u 0.199s 0:04.49 85.9% 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 Mon Oct 10 2011 at 17:04:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3734 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.658643 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 1.658643 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3539 net assigned charge : 5.300022 assigned positive charge : 561.4838 centred at (gu) : 92.40347 92.44518 92.92152 assigned negative charge : -556.1855 centred at (gu) : 92.78566 92.58042 92.85219 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 80812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33856 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24594 mr = 54243 m= 2653 mr = 16532 m= 94 mr = 1350 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 36025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 379 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 27215 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) : 0.5528809 object centre at (A) : 0.4155006 2.820000 58.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0704330E-03 1.7979317E-03 midg,1,midg; midg,igrid,midg 2.1463422E-02 -1.1907153E-02 1,midg,midg; igrid,midg,midg 1.9895183E-02 1.3562497E-04 gauss-seidel spectral radius is 0.9983209 estimated iterations to convergence 194 setup time was (sec) 0.9700000 now iterating at: 17:04:36 rms-change max change #iterations 3.895676 163.3501 at 10iterations 1.680666 62.23445 at 20iterations 0.7251921 24.87735 at 30iterations 0.3121967 10.01340 at 40iterations 0.1345753 4.346783 at 50iterations 5.8168236E-02 1.849846 at 60iterations 2.5131991E-02 0.8700943 at 70iterations 1.0900456E-02 0.3627801 at 80iterations 4.8081465E-03 0.1535110 at 90iterations 2.1814203E-03 6.7703247E-02 at 100iterations 1.0452829E-03 3.8295746E-02 at 110iterations 5.4799870E-04 1.8821716E-02 at 120iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 5.4799870E-04 1.8821716E-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) 8.290000 DelPhi exited at 17:04:45 8.295u 0.250s 0:10.11 84.4% 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 17:04:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3734 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.487964 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 2.487964 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3539 net assigned charge : 5.300022 assigned positive charge : 561.4838 centred at (gu) : 93.60500 93.66763 94.38194 assigned negative charge : -556.1855 centred at (gu) : 94.17844 93.87059 94.27822 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33856 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85428 mr = 133259 m= 24146 mr = 66789 m= 4259 mr = 17831 m= 384 mr = 2882 m= 9 mr = 186 m= 0 mr = 2 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 81221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 28285 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) : 1.658643 object centre at (A) : 0.4155006 2.820000 58.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1892209E-02 3.4393385E-02 midg,1,midg; midg,igrid,midg 0.8468075 -0.1270556 1,midg,midg; igrid,midg,midg 0.2811980 2.7991869E-02 gauss-seidel spectral radius is 0.9991965 estimated iterations to convergence 279 setup time was (sec) 1.830000 now iterating at: 17:04:47 rms-change max change #iterations 10.01330 263.6210 at 10iterations 5.751598 132.8664 at 20iterations 3.293713 74.42558 at 30iterations 1.875459 40.48925 at 40iterations 1.063568 21.47482 at 50iterations 0.6028304 12.12666 at 60iterations 0.3409356 8.703367 at 70iterations 0.1925050 4.083065 at 80iterations 0.1085232 2.455904 at 90iterations 6.1182171E-02 1.214249 at 100iterations 3.4490395E-02 0.6822319 at 110iterations 1.9409209E-02 0.4145517 at 120iterations 1.0949931E-02 0.2304096 at 130iterations 6.1885910E-03 0.1265373 at 140iterations 3.4948622E-03 7.2456360E-02 at 150iterations 1.9847762E-03 3.8685068E-02 at 160iterations 1.1412305E-03 2.2045135E-02 at 170iterations 6.6900428E-04 1.3772964E-02 at 180iterations finished qdiffx linear iterations at : 17:04:58 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 6.6900428E-04 1.3772964E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 17:04:59 13.236u 0.254s 0:14.13 95.3% 0+0k 0+0io 0pf+0w