Mon Oct 10 17:04:31 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 17:04:31 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HEM 819 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5047498 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 0.5047498 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 768.3831 centred at (gu) : 89.16648 90.05989 89.81639 assigned negative charge : -760.0887 centred at (gu) : 89.21249 90.02645 89.78016 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8137 nv = 96 ne = 84 npr = 103845 no. pairs analyzed = 103845 no. exposed pairs = 6371 no. arc points = 43580 no. surface atoms = 2157 nbur = 2963 mkacc time = 0.2200000 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 = 1.680000 m= 269 mr = 4214 m= 2 mr = 1 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 0.4800000 number of dielectric boundary points 4193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4295 ## 687 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1953908E-11 1.5905033E-10 midg,1,midg; midg,igrid,midg 1.7392816E-11 1.6357980E-10 1,midg,midg; igrid,midg,midg 2.3430571E-10 -6.9937203E-12 gauss-seidel spectral radius is 0.9799498 estimated iterations to convergence 58 setup time was (sec) 0.6900000 now iterating at: 17:04:32 rms-change max change #iterations 6.5813273E-02 10.38579 at 10iterations 5.7304744E-03 1.266098 at 20iterations 1.8396543E-03 0.4215927 at 30iterations 7.4332702E-04 0.1622810 at 40iterations 3.0586147E-04 6.3552856E-02 at 50iterations finished qdiffx linear iterations at : 17:04:34 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.0586147E-04 6.3552856E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 17:04:35 3.351u 0.159s 0:04.15 84.3% 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 17:04:35 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 = 5120 !!! WARNING: HEM 819 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.514249 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 1.514249 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 768.3831 centred at (gu) : 87.49799 90.17806 89.44754 assigned negative charge : -760.0887 centred at (gu) : 87.63738 90.07902 89.34016 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26034 mr = 64486 m= 2197 mr = 16846 m= 47 mr = 820 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 39200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 643 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 36495 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) : 0.5047498 object centre at (A) : 16.67850 3.072001 50.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8358678E-02 9.1052055E-03 midg,1,midg; midg,igrid,midg 1.9317182E-03 2.2785857E-03 1,midg,midg; igrid,midg,midg 1.4485123E-02 -2.3057400E-03 gauss-seidel spectral radius is 0.9980899 estimated iterations to convergence 182 setup time was (sec) 0.9000000 now iterating at: 17:04:36 rms-change max change #iterations 3.835965 183.2228 at 10iterations 1.558037 55.39687 at 20iterations 0.6366299 21.48368 at 30iterations 0.2598085 8.430252 at 40iterations 0.1061953 3.542530 at 50iterations 4.3626804E-02 1.420120 at 60iterations 1.8394828E-02 0.5674782 at 70iterations 8.1468942E-03 0.2852974 at 80iterations 4.0669390E-03 0.1690521 at 90iterations 2.3802160E-03 0.1138992 at 100iterations 1.5872672E-03 7.6557159E-02 at 110iterations 1.1318432E-03 5.2825928E-02 at 120iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.1318432E-03 5.2825928E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 17:04:44 7.630u 0.207s 0:09.13 85.7% 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 17:04:44 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 = 5120 !!! WARNING: HEM 819 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.271374 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 2.271374 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 768.3831 centred at (gu) : 86.24648 90.26682 89.17081 assigned negative charge : -760.0887 centred at (gu) : 86.45605 90.11843 89.01004 start vw surface at 0.2300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 217116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94546 mr = 158618 m= 22651 mr = 72934 m= 3068 mr = 15745 m= 178 mr = 1741 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 88465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 38765 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) : 1.514249 object centre at (A) : 16.67850 3.072001 50.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3689950 0.2335637 midg,1,midg; midg,igrid,midg 8.9416251E-02 -2.9410912E-06 1,midg,midg; igrid,midg,midg 0.2495286 -8.2062952E-02 gauss-seidel spectral radius is 0.9991634 estimated iterations to convergence 273 setup time was (sec) 1.840000 now iterating at: 17:04:47 rms-change max change #iterations 10.49815 306.8174 at 10iterations 6.053954 128.5847 at 20iterations 3.454225 85.70470 at 30iterations 1.964869 40.87547 at 40iterations 1.107826 26.22049 at 50iterations 0.6249368 15.67136 at 60iterations 0.3508462 7.651386 at 70iterations 0.1965475 3.725343 at 80iterations 0.1099429 2.303248 at 90iterations 6.1431795E-02 1.259171 at 100iterations 3.4325387E-02 0.6795683 at 110iterations 1.9228132E-02 0.3884583 at 120iterations 1.0781506E-02 0.2073631 at 130iterations 6.0955803E-03 0.1297150 at 140iterations 3.5072144E-03 7.2044373E-02 at 150iterations 2.0786000E-03 4.4113159E-02 at 160iterations 1.2960644E-03 3.0372620E-02 at 170iterations 8.6763711E-04 2.2289276E-02 at 180iterations finished qdiffx linear iterations at : 17:04:57 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 8.6763711E-04 2.2289276E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 17:04:58 12.076u 0.260s 0:13.15 93.7% 0+0k 0+0io 0pf+0w