Sun Oct 9 03:48:39 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 03:48:39 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4767 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 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: 0.5144657 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): -2.362000 60.46300 ymin,ymax (A): -12.17700 57.02100 zmin,zma (A): -15.64200 42.46100 x,y,z range (A): 62.82500 69.19800 58.10300 scale (grids/A): 0.5144657 object centre (A): 29.05050 22.42200 13.40950 number of atom coordinates read : 4767 total number of charged atoms : 4575 net assigned charge : 17.59999 assigned positive charge : 717.6162 centred at (gu) : 89.85848 92.29706 88.91827 assigned negative charge : -700.0220 centred at (gu) : 89.73158 92.37061 88.90088 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7899 nv = 96 ne = 84 npr = 96442 no. pairs analyzed = 96442 no. exposed pairs = 6099 no. arc points = 41937 no. surface atoms = 2046 nbur = 2721 mkacc time = 0.2100000 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= 312 mr = 3972 m= 0 mr = 5 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4155 ## 580 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2805450E-10 2.6782473E-10 midg,1,midg; midg,igrid,midg 2.8765226E-10 1.3476338E-10 1,midg,midg; igrid,midg,midg -8.5692529E-11 6.4729561E-10 gauss-seidel spectral radius is 0.9806766 estimated iterations to convergence 59 setup time was (sec) 0.7000000 now iterating at: 03:48:40 rms-change max change #iterations 6.8646789E-02 10.03041 at 10iterations 6.8040672E-03 0.9018555 at 20iterations 2.2534684E-03 0.2624445 at 30iterations 9.1463840E-04 0.1127710 at 40iterations 3.7959270E-04 4.8099518E-02 at 50iterations finished qdiffx linear iterations at : 03:48:42 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 3.7959270E-04 4.8099518E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 03:48:43 3.608u 0.209s 0:04.14 91.7% 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 Sun Oct 9 2011 at 03:48:43 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4767 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 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: 1.543397 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): -2.362000 60.46300 ymin,ymax (A): -12.17700 57.02100 zmin,zma (A): -15.64200 42.46100 x,y,z range (A): 62.82500 69.19800 58.10300 scale (grids/A): 1.543397 object centre (A): 29.05050 22.42200 13.40950 number of atom coordinates read : 4767 total number of charged atoms : 4575 net assigned charge : 17.59999 assigned positive charge : 717.6162 centred at (gu) : 89.57391 96.88956 86.75327 assigned negative charge : -700.0220 centred at (gu) : 89.19412 97.11169 86.70222 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25863 mr = 60389 m= 2154 mr = 16748 m= 43 mr = 806 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.6400000 number of dielectric boundary points 39538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 567 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 34470 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) : 0.5144657 object centre at (A) : 29.05050 22.42200 13.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3377068E-02 9.3452819E-03 midg,1,midg; midg,igrid,midg 2.8105428E-02 2.9379059E-02 1,midg,midg; igrid,midg,midg -8.5676415E-03 1.5215948E-02 gauss-seidel spectral radius is 0.9981475 estimated iterations to convergence 185 setup time was (sec) 0.9500000 now iterating at: 03:48:44 rms-change max change #iterations 3.860859 148.0281 at 10iterations 1.585691 59.13195 at 20iterations 0.6555828 22.49439 at 30iterations 0.2709813 8.777172 at 40iterations 0.1130539 3.744858 at 50iterations 4.7159061E-02 1.511705 at 60iterations 2.0240650E-02 0.6383743 at 70iterations 9.2904940E-03 0.2929897 at 80iterations 4.8119230E-03 0.1809788 at 90iterations 2.9292128E-03 9.5417023E-02 at 100iterations 2.0316096E-03 6.1817169E-02 at 110iterations 1.4875386E-03 4.3836594E-02 at 120iterations finished qdiffx linear iterations at : 03:48:51 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 1.4875386E-03 4.3836594E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 03:48:52 8.106u 0.245s 0:08.65 96.4% 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 Sun Oct 9 2011 at 03:48:52 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4767 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 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: 2.315096 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): -2.362000 60.46300 ymin,ymax (A): -12.17700 57.02100 zmin,zma (A): -15.64200 42.46100 x,y,z range (A): 62.82500 69.19800 58.10300 scale (grids/A): 2.315096 object centre (A): 29.05050 22.42200 13.40950 number of atom coordinates read : 4767 total number of charged atoms : 4575 net assigned charge : 17.59999 assigned positive charge : 717.6162 centred at (gu) : 89.36023 100.3339 85.12948 assigned negative charge : -700.0220 centred at (gu) : 88.79114 100.6675 85.05343 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 208448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92201 mr = 149015 m= 23159 mr = 70735 m= 2948 mr = 16231 m= 148 mr = 1621 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 448 time to turn everything in is 1.550000 number of dielectric boundary points 89283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 36523 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) : 1.543397 object centre at (A) : 29.05050 22.42200 13.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2290926 0.1520242 midg,1,midg; midg,igrid,midg 0.8197635 0.5326416 1,midg,midg; igrid,midg,midg -0.1467301 0.2457958 gauss-seidel spectral radius is 0.9991762 estimated iterations to convergence 275 setup time was (sec) 1.900000 now iterating at: 03:48:54 rms-change max change #iterations 10.34414 291.3143 at 10iterations 5.970339 145.1666 at 20iterations 3.408470 79.77134 at 30iterations 1.939094 44.63024 at 40iterations 1.100054 21.41082 at 50iterations 0.6203941 12.39290 at 60iterations 0.3488994 7.690849 at 70iterations 0.1960106 3.605003 at 80iterations 0.1101169 2.126557 at 90iterations 6.1860118E-02 1.163717 at 100iterations 3.4724552E-02 0.7434521 at 110iterations 1.9531449E-02 0.3664818 at 120iterations 1.1068500E-02 0.2225800 at 130iterations 6.3474770E-03 0.1194963 at 140iterations 3.7354999E-03 7.3265076E-02 at 150iterations 2.2986799E-03 4.6468735E-02 at 160iterations 1.5124149E-03 2.7729034E-02 at 170iterations 1.0745393E-03 2.0990372E-02 at 180iterations finished qdiffx linear iterations at : 03:49:05 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 1.0745393E-03 2.0990372E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 03:49:06 13.540u 0.246s 0:14.08 97.8% 0+0k 0+0io 0pf+0w