Sat Oct 15 13:57:18 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 Sat Oct 15 2011 at 13:57:19 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5131310 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): -16.06400 36.71800 ymin,ymax (A): -31.95500 31.47800 zmin,zma (A): -3.822000 65.55600 x,y,z range (A): 52.78200 63.43300 69.37800 scale (grids/A): 0.5131310 object centre (A): 10.32700 -0.2385006 30.86700 number of atom coordinates read : 4320 total number of charged atoms : 4118 net assigned charge : 0.9000351 assigned positive charge : 646.8002 centred at (gu) : 90.28751 90.69993 87.65231 assigned negative charge : -645.9041 centred at (gu) : 90.17240 90.75569 87.77738 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7144 nv = 96 ne = 84 npr = 88377 no. pairs analyzed = 88377 no. exposed pairs = 5528 no. arc points = 38964 no. surface atoms = 1858 nbur = 2462 mkacc time = 0.1400000 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 = 1.652000 m= 261 mr = 3627 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3752 ## 573 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9642 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1266486E-10 -1.7442660E-10 midg,1,midg; midg,igrid,midg 1.2451894E-10 -1.6843771E-10 1,midg,midg; igrid,midg,midg -2.7511862E-10 3.2417455E-10 gauss-seidel spectral radius is 0.9805436 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 13:57:20 rms-change max change #iterations 6.6346802E-02 9.776347 at 10iterations 3.8554631E-03 0.7340221 at 20iterations 2.7401064E-04 4.3922424E-02 at 30iterations 5.4183583E-05 6.6165924E-03 at 40iterations 1.7116346E-05 2.0383056E-03 at 50iterations finished qdiffx linear iterations at : 13:57:26 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.7116346E-05 2.0383056E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 13:57:27 3.998u 0.221s 0:08.25 51.0% 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 Sat Oct 15 2011 at 13:57:27 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.539393 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): -16.06400 36.71800 ymin,ymax (A): -31.95500 31.47800 zmin,zma (A): -3.822000 65.55600 x,y,z range (A): 52.78200 63.43300 69.37800 scale (grids/A): 1.539393 object centre (A): 10.32700 -0.2385006 30.86700 number of atom coordinates read : 4320 total number of charged atoms : 4118 net assigned charge : 0.9000351 assigned positive charge : 646.8002 centred at (gu) : 90.86114 92.09882 82.95546 assigned negative charge : -645.9041 centred at (gu) : 90.51676 92.26672 83.33190 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38964 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22904 mr = 54434 m= 1978 mr = 14964 m= 42 mr = 842 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 161 time to turn everything in is 0.4000000 number of dielectric boundary points 35172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 31063 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) : 0.5131310 object centre at (A) : 10.32700 -0.2385006 30.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2296904E-03 -1.4316406E-02 midg,1,midg; midg,igrid,midg 1.2744541E-05 -5.7242699E-03 1,midg,midg; igrid,midg,midg -3.1920625E-03 8.8810194E-03 gauss-seidel spectral radius is 0.9980888 estimated iterations to convergence 182 setup time was (sec) 0.6800000 now iterating at: 13:57:30 rms-change max change #iterations 3.606470 156.2360 at 10iterations 1.464363 53.89981 at 20iterations 0.5946779 19.55322 at 30iterations 0.2428522 8.527447 at 40iterations 9.8897226E-02 3.198391 at 50iterations 4.0450618E-02 1.428154 at 60iterations 1.6484402E-02 0.5552044 at 70iterations 6.7638289E-03 0.2158661 at 80iterations 2.7662497E-03 9.2559814E-02 at 90iterations 1.1377756E-03 3.8970947E-02 at 100iterations 4.6976184E-04 1.6292572E-02 at 110iterations 1.9971296E-04 6.2904358E-03 at 120iterations finished qdiffx linear iterations at : 13:57:44 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 1.9971296E-04 6.2904358E-03 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 13:57:45 8.877u 0.263s 0:17.62 51.8% 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 Sat Oct 15 2011 at 13:57:45 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.309089 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): -16.06400 36.71800 ymin,ymax (A): -31.95500 31.47800 zmin,zma (A): -3.822000 65.55600 x,y,z range (A): 52.78200 63.43300 69.37800 scale (grids/A): 2.309089 object centre (A): 10.32700 -0.2385006 30.86700 number of atom coordinates read : 4320 total number of charged atoms : 4118 net assigned charge : 0.9000351 assigned positive charge : 646.8002 centred at (gu) : 91.29140 93.14776 79.43283 assigned negative charge : -645.9041 centred at (gu) : 90.77501 93.39999 79.99785 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 187563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38964 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 82310 mr = 134000 m= 20181 mr = 63666 m= 2839 mr = 14119 m= 168 mr = 1746 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 611 time to turn everything in is 1.010000 number of dielectric boundary points 79466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 32850 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) : 1.539393 object centre at (A) : 10.32700 -0.2385006 30.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1559423 -0.2988493 midg,1,midg; midg,igrid,midg -5.3115591E-02 -0.1606296 1,midg,midg; igrid,midg,midg -4.2897277E-02 0.1248017 gauss-seidel spectral radius is 0.9991466 estimated iterations to convergence 270 setup time was (sec) 1.270000 now iterating at: 13:57:47 rms-change max change #iterations 9.773665 302.4692 at 10iterations 5.568736 146.9850 at 20iterations 3.151399 74.60778 at 30iterations 1.776155 39.53150 at 40iterations 0.9960788 22.09416 at 50iterations 0.5565985 12.53870 at 60iterations 0.3109248 7.637637 at 70iterations 0.1726187 3.598876 at 80iterations 9.5811240E-02 1.903667 at 90iterations 5.3175949E-02 1.141606 at 100iterations 2.9434694E-02 0.6108861 at 110iterations 1.6327456E-02 0.3184052 at 120iterations 9.0288511E-03 0.1840219 at 130iterations 4.9984353E-03 0.1024532 at 140iterations 2.7640124E-03 5.3766727E-02 at 150iterations 1.5260458E-03 2.9632092E-02 at 160iterations 8.4482413E-04 1.5808105E-02 at 170iterations 4.6614744E-04 1.0065079E-02 at 180iterations finished qdiffx linear iterations at : 13:58:11 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 4.6614744E-04 1.0065079E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.11000 DelPhi exited at 13:58:13 14.109u 0.265s 0:28.06 51.1% 0+0k 0+0io 0pf+0w