Mon Oct 10 17:15:51 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 Mon Oct 10 2011 at 17:15:51 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3019 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 0.5429230 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 0.5429230 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.471962 assigned positive charge : 457.9849 centred at (gu) : 90.48988 88.58831 91.28891 assigned negative charge : -462.4580 centred at (gu) : 90.52275 88.76256 91.40515 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5755 nv = 96 ne = 84 npr = 60051 no. pairs analyzed = 60051 no. exposed pairs = 4054 no. arc points = 28096 no. surface atoms = 1363 nbur = 1656 mkacc time = 0.1600000 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 = 1.596000 m= 226 mr = 2845 m= 0 mr = 10 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2517844E-10 -1.3478124E-09 midg,1,midg; midg,igrid,midg 1.1469251E-09 -9.4484842E-10 1,midg,midg; igrid,midg,midg -4.4552542E-11 -5.1063587E-10 gauss-seidel spectral radius is 0.9825189 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 17:15:52 rms-change max change #iterations 7.1835443E-02 12.51264 at 10iterations 4.7593727E-03 0.9690204 at 20iterations 3.0827383E-04 4.9658298E-02 at 30iterations 2.0664402E-05 4.0802956E-03 at 40iterations 1.4656542E-06 2.4414063E-04 at 50iterations finished qdiffx linear iterations at : 17:15:56 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 1.4656542E-06 2.4414063E-04 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 17:15:56 4.277u 0.258s 0:04.82 93.7% 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 Mon Oct 10 2011 at 17:15:56 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3019 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 1.628769 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 1.628769 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.471962 assigned positive charge : 457.9849 centred at (gu) : 91.46871 85.76415 93.86606 assigned negative charge : -462.4580 centred at (gu) : 91.56804 86.28712 94.21523 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17946 mr = 41647 m= 1621 mr = 11920 m= 42 mr = 709 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 736 time to turn everything in is 0.5200000 number of dielectric boundary points 28942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21984 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) : 0.5429230 object centre at (A) : 1.620502 0.2465000 -18.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6790815E-03 -8.5358778E-03 midg,1,midg; midg,igrid,midg 1.1899175E-02 -1.2291630E-02 1,midg,midg; igrid,midg,midg 1.7884291E-04 -2.5438922E-02 gauss-seidel spectral radius is 0.9981774 estimated iterations to convergence 186 setup time was (sec) 0.8400000 now iterating at: 17:15:57 rms-change max change #iterations 3.369202 174.5269 at 10iterations 1.392399 57.74471 at 20iterations 0.5783998 26.31458 at 30iterations 0.2403080 10.43865 at 40iterations 9.9839970E-02 3.461781 at 50iterations 4.1516069E-02 1.513134 at 60iterations 1.7166506E-02 0.6387329 at 70iterations 7.1647516E-03 0.2572441 at 80iterations 2.9804567E-03 0.1025639 at 90iterations 1.2386404E-03 4.3071508E-02 at 100iterations 5.1469571E-04 1.7982721E-02 at 110iterations 2.1474705E-04 7.7209473E-03 at 120iterations finished qdiffx linear iterations at : 17:16:06 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 2.1474705E-04 7.7209473E-03 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 17:16:06 9.342u 0.255s 0:09.87 97.1% 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 Mon Oct 10 2011 at 17:16:06 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3019 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 2.443153 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 2.443153 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.471962 assigned positive charge : 457.9849 centred at (gu) : 92.20267 83.64587 95.79868 assigned negative charge : -462.4580 centred at (gu) : 92.35196 84.43062 96.32269 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 148078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63808 mr = 102856 m= 16592 mr = 49244 m= 2353 mr = 12059 m= 138 mr = 1428 m= 0 mr = 63 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2532 time to turn everything in is 1.240000 number of dielectric boundary points 65319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 22984 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) : 1.628769 object centre at (A) : 1.620502 0.2465000 -18.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0831531E-02 -9.4984293E-02 midg,1,midg; midg,igrid,midg 0.1970497 -0.1748251 1,midg,midg; igrid,midg,midg 5.7262234E-02 -0.7495030 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 1.570000 now iterating at: 17:16:08 rms-change max change #iterations 8.835671 270.5687 at 10iterations 4.949183 153.4778 at 20iterations 2.762595 64.14840 at 30iterations 1.534556 34.22344 at 40iterations 0.8509079 23.03889 at 50iterations 0.4694475 9.466976 at 60iterations 0.2589995 6.269384 at 70iterations 0.1426630 2.778433 at 80iterations 7.8540847E-02 1.651914 at 90iterations 4.3189067E-02 0.9502100 at 100iterations 2.3755629E-02 0.4961777 at 110iterations 1.3045295E-02 0.2517509 at 120iterations 7.1702613E-03 0.1461182 at 130iterations 3.9435271E-03 8.0350876E-02 at 140iterations 2.1628016E-03 4.3693066E-02 at 150iterations 1.1878416E-03 2.3957968E-02 at 160iterations 6.5255060E-04 1.3508797E-02 at 170iterations 3.5887497E-04 7.2541237E-03 at 180iterations finished qdiffx linear iterations at : 17:16:21 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 3.5887497E-04 7.2541237E-03 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.05000 DelPhi exited at 17:16:22 15.056u 0.279s 0:15.85 96.6% 0+0k 0+0io 0pf+0w