Tue Oct 11 03:17:01 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 03:17:01 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 = 3402 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: 0.5348638 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 0.5348638 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3261 net assigned charge : -7.999983 assigned positive charge : 513.9982 centred at (gu) : 90.94765 88.01036 92.36853 assigned negative charge : -521.9997 centred at (gu) : 90.87557 87.95496 92.38260 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 68091 no. pairs analyzed = 68091 no. exposed pairs = 4267 no. arc points = 30391 no. surface atoms = 1419 nbur = 1983 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 = 1.596000 m= 298 mr = 3411 m= 1 mr = 13 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 0.3600000 number of dielectric boundary points 3283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3668604E-10 -6.9068329E-10 midg,1,midg; midg,igrid,midg -9.7930453E-10 -2.4900448E-11 1,midg,midg; igrid,midg,midg -5.3433474E-10 6.6539926E-11 gauss-seidel spectral radius is 0.9820201 estimated iterations to convergence 61 setup time was (sec) 0.6400000 now iterating at: 03:17:02 rms-change max change #iterations 7.1916014E-02 12.40029 at 10iterations 4.7571645E-03 0.7564783 at 20iterations 4.3314882E-04 5.9331894E-02 at 30iterations 8.3790903E-05 1.2821436E-02 at 40iterations 2.1138801E-05 3.4582615E-03 at 50iterations finished qdiffx linear iterations at : 03:17:05 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 2.1138801E-05 3.4582615E-03 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 03:17:06 3.993u 0.261s 0:05.00 85.0% 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 03:17:06 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 = 3402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.604591 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 1.604591 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3261 net assigned charge : -7.999983 assigned positive charge : 513.9982 centred at (gu) : 92.84196 84.03008 97.10474 assigned negative charge : -521.9997 centred at (gu) : 92.62584 83.86440 97.14713 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30391 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22689 mr = 49097 m= 2263 mr = 15606 m= 54 mr = 1079 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 940 time to turn everything in is 0.5800000 number of dielectric boundary points 30600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 441 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 24932 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) : 0.5348638 object centre at (A) : -15.25250 -26.26850 -1.738501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3406323E-02 -1.8654093E-02 midg,1,midg; midg,igrid,midg -8.1856130E-03 -3.4577158E-04 1,midg,midg; igrid,midg,midg -1.0715513E-02 -2.5439062E-03 gauss-seidel spectral radius is 0.9981577 estimated iterations to convergence 185 setup time was (sec) 0.9000000 now iterating at: 03:17:07 rms-change max change #iterations 3.502130 205.8147 at 10iterations 1.438512 56.75308 at 20iterations 0.5975609 20.98569 at 30iterations 0.2461691 8.848537 at 40iterations 0.1021853 3.433855 at 50iterations 4.2483307E-02 1.522629 at 60iterations 1.7694468E-02 0.6251564 at 70iterations 7.3406007E-03 0.2528210 at 80iterations 3.0816561E-03 0.1248991 at 90iterations 1.3086527E-03 4.3264333E-02 at 100iterations 5.6753930E-04 1.8701553E-02 at 110iterations 2.5859801E-04 8.9204311E-03 at 120iterations finished qdiffx linear iterations at : 03:17:14 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 2.5859801E-04 8.9204311E-03 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 03:17:14 7.589u 0.236s 0:08.38 93.1% 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 Tue Oct 11 2011 at 03:17:15 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 = 3402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.406887 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 2.406887 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3261 net assigned charge : -7.999983 assigned positive charge : 513.9982 centred at (gu) : 94.26258 81.04498 100.6569 assigned negative charge : -521.9997 centred at (gu) : 93.93856 80.79652 100.7207 start vw surface at 0.2300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 165961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30391 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 78443 mr = 119823 m= 22323 mr = 62531 m= 3558 mr = 16737 m= 208 mr = 2205 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 3158 time to turn everything in is 1.300000 number of dielectric boundary points 69133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 26044 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) : 1.604591 object centre at (A) : -15.25250 -26.26850 -1.738501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4379930 -0.3831853 midg,1,midg; midg,igrid,midg -7.6911487E-02 2.1748727E-02 1,midg,midg; igrid,midg,midg -0.1483659 -2.3035191E-02 gauss-seidel spectral radius is 0.9991370 estimated iterations to convergence 269 setup time was (sec) 1.600000 now iterating at: 03:17:16 rms-change max change #iterations 9.116710 264.8989 at 10iterations 5.124786 129.8054 at 20iterations 2.851113 69.80834 at 30iterations 1.586549 34.18179 at 40iterations 0.8811855 17.56114 at 50iterations 0.4873768 9.839209 at 60iterations 0.2689976 5.141724 at 70iterations 0.1490819 3.234362 at 80iterations 8.2127072E-02 1.864208 at 90iterations 4.5222767E-02 0.9624906 at 100iterations 2.4942776E-02 0.4959414 at 110iterations 1.3735720E-02 0.2814145 at 120iterations 7.5537418E-03 0.1672611 at 130iterations 4.1597490E-03 8.2466125E-02 at 140iterations 2.2925618E-03 4.6947479E-02 at 150iterations 1.2668213E-03 2.4794579E-02 at 160iterations 6.9942244E-04 1.3687134E-02 at 170iterations 3.8843416E-04 8.2741380E-03 at 180iterations finished qdiffx linear iterations at : 03:17:27 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 3.8843416E-04 8.2741380E-03 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 03:17:27 12.093u 0.243s 0:12.62 97.7% 0+0k 0+0io 0pf+0w