Wed Dec 21 14:21:44 PST 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 Wed Dec 21 2011 at 14:21:44 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6640304 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 0.6640304 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 4.8577785E-06 assigned positive charge : 296.8839 centred at (gu) : 91.07784 92.65816 90.22781 assigned negative charge : -296.8843 centred at (gu) : 91.21371 92.75614 90.15382 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6098 nv = 96 ne = 84 npr = 41619 no. pairs analyzed = 41619 no. exposed pairs = 2371 no. arc points = 17032 no. surface atoms = 807 nbur = 1197 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3517 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.1700000 number of dielectric boundary points 2868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1077667E-08 1.3586221E-08 midg,1,midg; midg,igrid,midg 9.7077120E-09 -2.7762503E-08 1,midg,midg; igrid,midg,midg 1.8346109E-08 -2.7831977E-08 gauss-seidel spectral radius is 0.9881906 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 14:21:45 rms-change max change #iterations 0.1544208 25.72136 at 10iterations 1.6586259E-02 2.340683 at 20iterations 1.7923649E-03 0.2743645 at 30iterations 1.9237478E-04 3.2745361E-02 at 40iterations 2.0436584E-05 2.7022362E-03 at 50iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 2.0436584E-05 2.7022362E-03 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 14:22:19 4.662u 0.256s 0:35.49 13.8% 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 Wed Dec 21 2011 at 14:22:21 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.992091 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 1.992091 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 4.8577785E-06 assigned positive charge : 296.8839 centred at (gu) : 93.23311 97.97430 90.68333 assigned negative charge : -296.8843 centred at (gu) : 93.64126 98.26837 90.46152 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17032 grid for indexing accessible points = 1.400000 m= 25430 mr = 45333 m= 4459 mr = 19938 m= 284 mr = 3021 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1900 time to turn everything in is 0.3500000 number of dielectric boundary points 26508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14805 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) : 0.6640304 object centre at (A) : 14.18000 22.68450 3.277000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7948206E-02 1.1605009E-02 midg,1,midg; midg,igrid,midg 3.3875711E-02 -1.3999154E-02 1,midg,midg; igrid,midg,midg 8.7998910E-03 -1.3688456E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.5700000 now iterating at: 14:22:23 rms-change max change #iterations 3.990191 189.7912 at 10iterations 1.893094 72.57791 at 20iterations 0.9000012 29.02140 at 30iterations 0.4251227 15.00063 at 40iterations 0.2010740 7.171800 at 50iterations 9.5326103E-02 3.230865 at 60iterations 4.5171540E-02 1.643078 at 70iterations 2.1291936E-02 0.7245293 at 80iterations 1.0090572E-02 0.3333321 at 90iterations 4.7862064E-03 0.1543121 at 100iterations 2.2588572E-03 7.0606232E-02 at 110iterations 1.0733948E-03 3.5676956E-02 at 120iterations finished qdiffx linear iterations at : 14:22:33 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 1.0733948E-03 3.5676956E-02 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.21000 DelPhi exited at 14:22:42 10.209u 0.300s 0:21.18 49.5% 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 Wed Dec 21 2011 at 14:22:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.988137 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 2.988137 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 4.8577785E-06 assigned positive charge : 296.8839 centred at (gu) : 94.84969 101.9615 91.02492 assigned negative charge : -296.8843 centred at (gu) : 95.46188 102.4027 90.69231 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17032 grid for indexing accessible points = 1.400000 m= 80002 mr = 109059 m= 32238 mr = 67611 m= 8181 mr = 27157 m= 1245 mr = 6559 m= 77 mr = 861 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 6779 time to turn everything in is 0.8600000 number of dielectric boundary points 59716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14967 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) : 1.992091 object centre at (A) : 14.18000 22.68450 3.277000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8104319 -1.8651824E-02 midg,1,midg; midg,igrid,midg 0.3182712 -0.2161898 1,midg,midg; igrid,midg,midg 3.6559347E-02 -8.9517005E-02 gauss-seidel spectral radius is 0.9992561 estimated iterations to convergence 289 setup time was (sec) 1.110000 now iterating at: 14:22:47 rms-change max change #iterations 9.163141 523.3895 at 10iterations 5.251757 119.0896 at 20iterations 3.010948 62.98152 at 30iterations 1.726567 32.59102 at 40iterations 0.9905810 21.30375 at 50iterations 0.5664086 10.86852 at 60iterations 0.3248006 5.974800 at 70iterations 0.1853652 3.526502 at 80iterations 0.1063156 2.191693 at 90iterations 6.0737390E-02 1.090488 at 100iterations 3.4830235E-02 0.6250820 at 110iterations 1.9955490E-02 0.3944893 at 120iterations 1.1421089E-02 0.2408524 at 130iterations 6.5240446E-03 0.1215992 at 140iterations 3.7447864E-03 6.6310883E-02 at 150iterations 2.1429579E-03 3.9138794E-02 at 160iterations 1.2263866E-03 2.4135590E-02 at 170iterations 7.0244673E-04 1.3046265E-02 at 180iterations finished qdiffx linear iterations at : 14:23:02 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 7.0244673E-04 1.3046265E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 14:23:05 15.505u 0.259s 0:20.48 76.9% 0+0k 0+0io 0pf+0w