Tue Oct 11 03:16:44 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 03:16:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 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: 0.5376669 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): -14.93900 48.61500 ymin,ymax (A): -19.24100 44.02100 zmin,zma (A): 19.11300 85.32500 x,y,z range (A): 63.55400 63.26200 66.21201 scale (grids/A): 0.5376669 object centre (A): 16.83800 12.39000 52.21900 number of atom coordinates read : 5176 total number of charged atoms : 5035 net assigned charge : 2.500016 assigned positive charge : 796.4506 centred at (gu) : 90.24490 90.45977 90.11397 assigned negative charge : -793.9571 centred at (gu) : 90.24232 90.44132 90.16035 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9368 nv = 96 ne = 84 npr = 105969 no. pairs analyzed = 105969 no. exposed pairs = 6145 no. arc points = 42346 no. surface atoms = 2059 nbur = 3117 mkacc time = 0.1800000 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 = 1.568000 m= 322 mr = 5084 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3400000 number of dielectric boundary points 4596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4231 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9628485E-10 -3.0158523E-10 midg,1,midg; midg,igrid,midg -4.2844617E-11 3.0395170E-10 1,midg,midg; igrid,midg,midg 8.4011506E-11 1.4194422E-10 gauss-seidel spectral radius is 0.9823273 estimated iterations to convergence 62 setup time was (sec) 0.5300000 now iterating at: 03:16:45 rms-change max change #iterations 9.6497849E-02 12.19077 at 10iterations 6.4292289E-03 0.8315821 at 20iterations 8.1417459E-04 0.1084633 at 30iterations 2.6271224E-04 3.5591125E-02 at 40iterations 9.7837503E-05 1.3343811E-02 at 50iterations finished qdiffx linear iterations at : 03:16:48 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 9.7837503E-05 1.3343811E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 03:16:48 3.555u 0.177s 0:04.02 92.5% 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 Tue Oct 11 2011 at 03:16:48 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 = 5176 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.613001 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): -14.93900 48.61500 ymin,ymax (A): -19.24100 44.02100 zmin,zma (A): 19.11300 85.32500 x,y,z range (A): 63.55400 63.26200 66.21201 scale (grids/A): 1.613001 object centre (A): 16.83800 12.39000 52.21900 number of atom coordinates read : 5176 total number of charged atoms : 5035 net assigned charge : 2.500016 assigned positive charge : 796.4506 centred at (gu) : 90.73267 91.37748 90.34011 assigned negative charge : -793.9571 centred at (gu) : 90.72655 91.32356 90.48083 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 105145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32571 mr = 74005 m= 3356 mr = 22786 m= 101 mr = 1553 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3272 time to turn everything in is 0.4900000 number of dielectric boundary points 42825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 448 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 38491 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) : 0.5376669 object centre at (A) : 16.83800 12.39000 52.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4477503E-03 1.2322643E-03 midg,1,midg; midg,igrid,midg 1.4771797E-02 2.3569895E-02 1,midg,midg; igrid,midg,midg -7.5511271E-05 5.3801639E-03 gauss-seidel spectral radius is 0.9983532 estimated iterations to convergence 196 setup time was (sec) 0.7100000 now iterating at: 03:16:49 rms-change max change #iterations 4.560396 159.2380 at 10iterations 1.977052 60.98297 at 20iterations 0.8579711 26.21847 at 30iterations 0.3738101 10.93889 at 40iterations 0.1627770 4.957858 at 50iterations 7.1205147E-02 2.090586 at 60iterations 3.1048952E-02 0.8968277 at 70iterations 1.3588972E-02 0.3948174 at 80iterations 5.9695896E-03 0.1591077 at 90iterations 2.6691242E-03 7.6726913E-02 at 100iterations 1.2446862E-03 3.6453247E-02 at 110iterations 6.1718916E-04 2.0289660E-02 at 120iterations finished qdiffx linear iterations at : 03:16:57 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 6.1718916E-04 2.0289660E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 03:16:57 8.058u 0.219s 0:08.64 95.6% 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 03:16:57 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 = 5176 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: 2.419501 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): -14.93900 48.61500 ymin,ymax (A): -19.24100 44.02100 zmin,zma (A): 19.11300 85.32500 x,y,z range (A): 63.55400 63.26200 66.21201 scale (grids/A): 2.419501 object centre (A): 16.83800 12.39000 52.21900 number of atom coordinates read : 5176 total number of charged atoms : 5035 net assigned charge : 2.500016 assigned positive charge : 796.4506 centred at (gu) : 91.09859 92.06532 90.50984 assigned negative charge : -793.9571 centred at (gu) : 91.08979 91.98505 90.72113 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 244900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 113804 mr = 180972 m= 32208 mr = 91135 m= 5148 mr = 24252 m= 386 mr = 3275 m= 5 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 10731 time to turn everything in is 1.240000 number of dielectric boundary points 96652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 40233 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) : 1.613001 object centre at (A) : 16.83800 12.39000 52.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1621189 8.1299439E-02 midg,1,midg; midg,igrid,midg 0.1917124 0.3360985 1,midg,midg; igrid,midg,midg 4.9097970E-02 0.1052269 gauss-seidel spectral radius is 0.9992385 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 03:16:59 rms-change max change #iterations 11.79527 305.0720 at 10iterations 6.936843 145.4635 at 20iterations 4.061073 81.90343 at 30iterations 2.360543 46.97472 at 40iterations 1.367170 25.90345 at 50iterations 0.7899258 15.12171 at 60iterations 0.4552646 8.118234 at 70iterations 0.2621034 4.608000 at 80iterations 0.1506878 2.548039 at 90iterations 8.6421140E-02 1.516654 at 100iterations 4.9619522E-02 0.8194973 at 110iterations 2.8434340E-02 0.4839325 at 120iterations 1.6339174E-02 0.3035862 at 130iterations 9.4076004E-03 0.1657391 at 140iterations 5.4160273E-03 8.8768005E-02 at 150iterations 3.1488112E-03 5.4866791E-02 at 160iterations 1.8519459E-03 3.4842491E-02 at 170iterations 1.1110997E-03 1.9438744E-02 at 180iterations finished qdiffx linear iterations at : 03:17:11 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.1110997E-03 1.9438744E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 03:17:11 13.577u 0.220s 0:14.14 97.5% 0+0k 0+0io 0pf+0w