Tue Oct 11 06:58:12 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 06:58:12 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 = 2981 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: 0.5609833 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 0.5609833 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2842 net assigned charge : -0.4999878 assigned positive charge : 436.7694 centred at (gu) : 89.85016 90.25144 89.88563 assigned negative charge : -437.2701 centred at (gu) : 89.83663 90.42477 89.90007 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6078 nv = 96 ne = 84 npr = 61772 no. pairs analyzed = 61772 no. exposed pairs = 3773 no. arc points = 26810 no. surface atoms = 1275 nbur = 1706 mkacc time = 0.2000000 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 = 1.540000 m= 274 mr = 3159 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 7822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1843386E-10 -2.0541555E-10 midg,1,midg; midg,igrid,midg 1.7568678E-09 -2.1783795E-09 1,midg,midg; igrid,midg,midg -2.0821812E-10 1.0087880E-10 gauss-seidel spectral radius is 0.9836106 estimated iterations to convergence 64 setup time was (sec) 0.7700000 now iterating at: 06:58:13 rms-change max change #iterations 8.5526168E-02 14.92981 at 10iterations 6.1039361E-03 0.9597225 at 20iterations 5.2264694E-04 9.3124390E-02 at 30iterations 7.2747025E-05 1.8039703E-02 at 40iterations 1.5037916E-05 3.9978027E-03 at 50iterations finished qdiffx linear iterations at : 06:58:17 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.5037916E-05 3.9978027E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 06:58:18 4.899u 0.445s 0:06.22 85.6% 0+0k 0+0io 5pf+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 06:58:18 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 = 2981 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: 1.682950 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 1.682950 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2842 net assigned charge : -0.4999878 assigned positive charge : 436.7694 centred at (gu) : 89.54974 90.75353 89.65643 assigned negative charge : -437.2701 centred at (gu) : 89.50929 91.27412 89.69981 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26810 grid for indexing accessible points = 1.400000 m= 22635 mr = 43656 m= 2885 mr = 16260 m= 78 mr = 1662 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 29723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21886 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) : 0.5609833 object centre at (A) : 12.28500 47.12300 -45.57900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7732573E-03 1.0941690E-02 midg,1,midg; midg,igrid,midg 2.7409892E-03 -2.2522970E-03 1,midg,midg; igrid,midg,midg 8.2173217E-03 -1.4593433E-02 gauss-seidel spectral radius is 0.9983015 estimated iterations to convergence 193 setup time was (sec) 1.110000 now iterating at: 06:58:20 rms-change max change #iterations 3.513006 172.2404 at 10iterations 1.506723 58.16286 at 20iterations 0.6441888 25.05895 at 30iterations 0.2769085 11.66318 at 40iterations 0.1188820 4.325981 at 50iterations 5.1233888E-02 2.036369 at 60iterations 2.1901550E-02 0.8517208 at 70iterations 9.4123771E-03 0.3085175 at 80iterations 4.0497882E-03 0.1326495 at 90iterations 1.7443576E-03 5.9152603E-02 at 100iterations 7.5470901E-04 2.5598526E-02 at 110iterations 3.2891403E-04 1.2456894E-02 at 120iterations finished qdiffx linear iterations at : 06:58:30 total time elapsed so far: 10.86000 # loops : 120 mean,max change (kT/e) : 3.2891403E-04 1.2456894E-02 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 06:58:30 11.082u 0.484s 0:12.16 95.0% 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 06:58:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2981 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: 2.524425 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 2.524425 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2842 net assigned charge : -0.4999878 assigned positive charge : 436.7694 centred at (gu) : 89.32442 91.13011 89.48443 assigned negative charge : -437.2701 centred at (gu) : 89.26392 91.91095 89.54960 start vw surface at 0.1800000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 152019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26810 grid for indexing accessible points = 1.400000 m= 73940 mr = 106408 m= 25296 mr = 59375 m= 4862 mr = 20043 m= 378 mr = 3425 m= 6 mr = 178 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 67074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 22709 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) : 1.682950 object centre at (A) : 12.28500 47.12300 -45.57900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1365218 0.2240976 midg,1,midg; midg,igrid,midg 2.1924367E-02 -3.0427678E-02 1,midg,midg; igrid,midg,midg 0.1186661 -6.6714361E-02 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 2.300000 now iterating at: 06:58:33 rms-change max change #iterations 8.867349 363.5419 at 10iterations 5.031827 138.7263 at 20iterations 2.834674 68.14025 at 30iterations 1.594632 35.76064 at 40iterations 0.8938437 17.89736 at 50iterations 0.5020993 10.91772 at 60iterations 0.2804905 6.376922 at 70iterations 0.1562022 3.315872 at 80iterations 8.7344348E-02 1.779959 at 90iterations 4.8622042E-02 0.9783783 at 100iterations 2.7173625E-02 0.5894279 at 110iterations 1.5098569E-02 0.3141279 at 120iterations 8.4178559E-03 0.1703663 at 130iterations 4.6893205E-03 0.1041155 at 140iterations 2.6138441E-03 4.8843384E-02 at 150iterations 1.4554822E-03 2.9544115E-02 at 160iterations 8.1417791E-04 1.7913818E-02 at 170iterations 4.5660796E-04 8.6696446E-03 at 180iterations finished qdiffx linear iterations at : 06:58:50 total time elapsed so far: 18.61000 # loops : 180 mean,max change (kT/e) : 4.5660796E-04 8.6696446E-03 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.83000 DelPhi exited at 06:58:50 18.836u 0.512s 0:19.88 97.2% 0+0k 0+0io 0pf+0w