Tue Oct 11 06:07:45 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 06:07:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 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: 0.7477421 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 0.7477421 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1924 net assigned charge : 6.500006 assigned positive charge : 310.5250 centred at (gu) : 90.18988 90.28519 91.25964 assigned negative charge : -304.0252 centred at (gu) : 90.36590 90.24876 91.35388 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 40701 no. pairs analyzed = 40701 no. exposed pairs = 2447 no. arc points = 16814 no. surface atoms = 840 nbur = 1195 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 596 mr = 4661 m= 8 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1412 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9265397E-07 3.5600600E-08 midg,1,midg; midg,igrid,midg 9.1322974E-08 1.8749826E-07 1,midg,midg; igrid,midg,midg 3.2065967E-07 -6.7204958E-08 gauss-seidel spectral radius is 0.9906639 estimated iterations to convergence 84 setup time was (sec) 0.3500000 now iterating at: 06:07:45 rms-change max change #iterations 0.2533312 29.47364 at 10iterations 3.5082668E-02 4.442486 at 20iterations 4.8751719E-03 0.6177101 at 30iterations 7.6836109E-04 9.8576546E-02 at 40iterations 1.5925609E-04 2.1636009E-02 at 50iterations finished qdiffx linear iterations at : 06:07:48 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.5925609E-04 2.1636009E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:07:49 3.364u 0.184s 0:04.24 83.4% 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 Tue Oct 11 2011 at 06:07:49 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 = 2035 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: 2.243226 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 2.243226 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1924 net assigned charge : 6.500006 assigned positive charge : 310.5250 centred at (gu) : 90.56942 90.85587 93.77879 assigned negative charge : -304.0252 centred at (gu) : 91.09753 90.74626 94.06181 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 82572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 35258 mr = 59371 m= 7895 mr = 27392 m= 879 mr = 5598 m= 41 mr = 489 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 33788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15328 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) : 0.7477421 object centre at (A) : 25.17500 20.91100 21.08400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7244914E-02 3.2955725E-02 midg,1,midg; midg,igrid,midg 4.5023477E-03 4.3337636E-02 1,midg,midg; igrid,midg,midg 6.0440257E-02 2.2024471E-02 gauss-seidel spectral radius is 0.9989319 estimated iterations to convergence 242 setup time was (sec) 0.6200000 now iterating at: 06:07:50 rms-change max change #iterations 4.996992 192.1852 at 10iterations 2.557125 84.77395 at 20iterations 1.313582 40.50236 at 30iterations 0.6754550 18.70432 at 40iterations 0.3469345 10.47294 at 50iterations 0.1774241 5.168182 at 60iterations 9.0599470E-02 2.956381 at 70iterations 4.6564307E-02 1.364876 at 80iterations 2.3930252E-02 0.6743145 at 90iterations 1.2310665E-02 0.3315125 at 100iterations 6.3698599E-03 0.1729259 at 110iterations 3.3166313E-03 0.1045742 at 120iterations finished qdiffx linear iterations at : 06:07:57 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 3.3166313E-03 0.1045742 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 06:07:58 7.913u 0.223s 0:08.82 92.1% 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 06:07:58 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 = 2035 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: 3.364839 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 3.364839 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1924 net assigned charge : 6.500006 assigned positive charge : 310.5250 centred at (gu) : 90.85399 91.28384 95.66812 assigned negative charge : -304.0252 centred at (gu) : 91.64637 91.11946 96.09273 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 107059 mr = 142351 m= 47433 mr = 90188 m= 15349 mr = 39757 m= 3492 mr = 12334 m= 545 mr = 2643 m= 28 mr = 376 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 76252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15392 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) : 2.243226 object centre at (A) : 25.17500 20.91100 21.08400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3572988 0.3765753 midg,1,midg; midg,igrid,midg -1.4242111E-02 0.3150648 1,midg,midg; igrid,midg,midg 0.4333864 0.3560576 gauss-seidel spectral radius is 0.9993188 estimated iterations to convergence 302 setup time was (sec) 1.540000 now iterating at: 06:08:00 rms-change max change #iterations 10.86903 273.1313 at 10iterations 6.522199 138.1929 at 20iterations 3.895707 96.66302 at 30iterations 2.324285 45.31257 at 40iterations 1.385024 27.55076 at 50iterations 0.8227940 15.23713 at 60iterations 0.4872096 9.267507 at 70iterations 0.2890781 4.646866 at 80iterations 0.1712675 3.039408 at 90iterations 0.1009081 1.649455 at 100iterations 5.9795130E-02 1.024712 at 110iterations 3.5480231E-02 0.5593081 at 120iterations 2.1095300E-02 0.3284149 at 130iterations 1.2621718E-02 0.2652969 at 140iterations 7.6558525E-03 0.1393509 at 150iterations 4.7550150E-03 8.2145691E-02 at 160iterations 3.0489455E-03 4.8678398E-02 at 170iterations 2.0735592E-03 3.3384323E-02 at 180iterations finished qdiffx linear iterations at : 06:08:11 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.0735592E-03 3.3384323E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 06:08:11 13.171u 0.215s 0:13.68 97.8% 0+0k 0+0io 0pf+0w