Tue Oct 11 05:30:21 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 Tue Oct 11 2011 at 05:30:21 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6782761 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 0.6782761 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 90.64127 90.26999 89.65804 assigned negative charge : -313.8622 centred at (gu) : 90.77783 90.26072 89.71850 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 41971 no. pairs analyzed = 41971 no. exposed pairs = 2580 no. arc points = 17407 no. surface atoms = 879 nbur = 1411 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3745 m= 5 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1710 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7456 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0976762E-08 7.3074196E-09 midg,1,midg; midg,igrid,midg 1.9700201E-08 2.6827065E-08 1,midg,midg; igrid,midg,midg 5.0149186E-08 -1.3745986E-08 gauss-seidel spectral radius is 0.9886786 estimated iterations to convergence 77 setup time was (sec) 0.5000000 now iterating at: 05:30:22 rms-change max change #iterations 0.1704695 25.23925 at 10iterations 1.9882739E-02 3.163498 at 20iterations 2.7764426E-03 0.4020729 at 30iterations 5.4910686E-04 7.2601318E-02 at 40iterations 1.5216200E-04 1.7675400E-02 at 50iterations finished qdiffx linear iterations at : 05:30:25 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.5216200E-04 1.7675400E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 05:30:25 3.288u 0.193s 0:03.80 91.3% 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 Tue Oct 11 2011 at 05:30:25 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.034828 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 2.034828 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 91.92395 90.80980 88.97391 assigned negative charge : -313.8622 centred at (gu) : 92.33352 90.78217 89.15561 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 27259 mr = 49188 m= 4878 mr = 20581 m= 380 mr = 3145 m= 16 mr = 164 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 28684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15528 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) : 0.6782761 object centre at (A) : 24.18150 21.04350 23.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3648712E-02 5.0962720E-02 midg,1,midg; midg,igrid,midg 1.7225334E-03 2.1076862E-02 1,midg,midg; igrid,midg,midg 2.6105605E-02 -5.6824014E-03 gauss-seidel spectral radius is 0.9987404 estimated iterations to convergence 223 setup time was (sec) 0.8100000 now iterating at: 05:30:26 rms-change max change #iterations 4.280811 195.2399 at 10iterations 2.075054 68.06756 at 20iterations 1.005687 34.35040 at 30iterations 0.4839001 15.87180 at 40iterations 0.2351676 7.821568 at 50iterations 0.1140152 3.777915 at 60iterations 5.5243809E-02 1.897705 at 70iterations 2.6915776E-02 0.8416481 at 80iterations 1.3254032E-02 0.4097853 at 90iterations 6.5760161E-03 0.2056732 at 100iterations 3.3167864E-03 0.1100502 at 110iterations 1.7578931E-03 5.2890778E-02 at 120iterations finished qdiffx linear iterations at : 05:30:33 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.7578931E-03 5.2890778E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 05:30:33 7.344u 0.217s 0:07.85 96.1% 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 05:30:33 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.052243 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 3.052243 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 92.88591 91.21478 88.46091 assigned negative charge : -313.8622 centred at (gu) : 93.50040 91.17327 88.73345 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 159663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 86006 mr = 118465 m= 33634 mr = 71476 m= 9023 mr = 27553 m= 1566 mr = 6822 m= 141 mr = 1057 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 64594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 15720 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) : 2.034828 object centre at (A) : 24.18150 21.04350 23.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3452343 0.7583943 midg,1,midg; midg,igrid,midg -1.4647501E-02 0.1888932 1,midg,midg; igrid,midg,midg 0.2280426 -7.6678637E-03 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.690000 now iterating at: 05:30:35 rms-change max change #iterations 9.780130 323.4900 at 10iterations 5.748575 178.6441 at 20iterations 3.381020 74.83669 at 30iterations 1.977124 38.81686 at 40iterations 1.150165 23.55188 at 50iterations 0.6724736 15.59926 at 60iterations 0.3913845 8.311184 at 70iterations 0.2279392 5.069164 at 80iterations 0.1324114 2.528255 at 90iterations 7.7073582E-02 1.387741 at 100iterations 4.5046821E-02 0.8326006 at 110iterations 2.6443698E-02 0.5658073 at 120iterations 1.5638335E-02 0.3074055 at 130iterations 9.4452258E-03 0.1839790 at 140iterations 5.8624027E-03 0.1086121 at 150iterations 3.8126495E-03 8.7249756E-02 at 160iterations 2.6275502E-03 5.0056458E-02 at 170iterations 1.9139006E-03 3.4217834E-02 at 180iterations finished qdiffx linear iterations at : 05:30:45 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 1.9139006E-03 3.4217834E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 05:30:46 12.032u 0.213s 0:12.53 97.6% 0+0k 0+0io 0pf+0w