Mon Oct 10 16:04:48 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 Mon Oct 10 2011 at 16:04:48 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 = 5142 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5041493 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): 7.447000 62.63600 ymin,ymax (A): -28.96000 41.65400 zmin,zma (A): -29.09600 33.56100 x,y,z range (A): 55.18900 70.61401 62.65700 scale (grids/A): 0.5041493 object centre (A): 35.04150 6.347001 2.232501 number of atom coordinates read : 5142 total number of charged atoms : 4981 net assigned charge : 0.5000154 assigned positive charge : 773.4487 centred at (gu) : 89.67953 89.24283 88.95408 assigned negative charge : -772.9541 centred at (gu) : 89.63384 89.23385 88.95231 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8114 nv = 96 ne = 84 npr = 105282 no. pairs analyzed = 105282 no. exposed pairs = 6343 no. arc points = 42035 no. surface atoms = 2144 nbur = 2998 mkacc time = 0.2800000 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 = 1.680000 m= 282 mr = 4364 m= 0 mr = 9 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4084 ## 590 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6563779E-12 7.2707665E-12 midg,1,midg; midg,igrid,midg -1.6334913E-11 2.0283516E-11 1,midg,midg; igrid,midg,midg -1.0001292E-10 9.3645112E-11 gauss-seidel spectral radius is 0.9798990 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 16:04:49 rms-change max change #iterations 6.6400379E-02 9.077093 at 10iterations 4.7502625E-03 0.6783104 at 20iterations 1.1830498E-03 0.1681976 at 30iterations 4.6352195E-04 6.1607361E-02 at 40iterations 1.9029286E-04 2.5644302E-02 at 50iterations finished qdiffx linear iterations at : 16:04:53 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.9029286E-04 2.5644302E-02 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.810000 DelPhi exited at 16:04:54 4.814u 0.406s 0:05.51 94.5% 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 Mon Oct 10 2011 at 16:04:54 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 = 5142 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.512448 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): 7.447000 62.63600 ymin,ymax (A): -28.96000 41.65400 zmin,zma (A): -29.09600 33.56100 x,y,z range (A): 55.18900 70.61401 62.65700 scale (grids/A): 1.512448 object centre (A): 35.04150 6.347001 2.232501 number of atom coordinates read : 5142 total number of charged atoms : 4981 net assigned charge : 0.5000154 assigned positive charge : 773.4487 centred at (gu) : 89.03691 87.72628 86.86035 assigned negative charge : -772.9541 centred at (gu) : 88.90098 87.70097 86.85650 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 93682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42035 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27149 mr = 66060 m= 2107 mr = 18293 m= 26 mr = 854 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 843 time to turn everything in is 0.7700000 number of dielectric boundary points 37757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 534 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 37268 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) : 0.5041493 object centre at (A) : 35.04150 6.347001 2.232501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5653486E-04 -8.0681816E-03 midg,1,midg; midg,igrid,midg 1.4669755E-02 2.7034231E-03 1,midg,midg; igrid,midg,midg -3.0877086E-04 2.1998987E-03 gauss-seidel spectral radius is 0.9980819 estimated iterations to convergence 181 setup time was (sec) 1.070000 now iterating at: 16:04:55 rms-change max change #iterations 3.834836 162.8409 at 10iterations 1.555017 50.85899 at 20iterations 0.6325514 21.42018 at 30iterations 0.2588594 9.117049 at 40iterations 0.1057248 3.292667 at 50iterations 4.3307230E-02 1.366730 at 60iterations 1.7954508E-02 0.5805597 at 70iterations 7.6264855E-03 0.2454200 at 80iterations 3.4935649E-03 0.1120758 at 90iterations 1.8100464E-03 6.5483093E-02 at 100iterations 1.1076613E-03 3.2806396E-02 at 110iterations 7.5413310E-04 1.9893646E-02 at 120iterations finished qdiffx linear iterations at : 16:05:05 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 7.5413310E-04 1.9893646E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 16:05:05 10.963u 0.436s 0:11.67 97.6% 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 Mon Oct 10 2011 at 16:05:05 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 = 5142 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.268672 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): 7.447000 62.63600 ymin,ymax (A): -28.96000 41.65400 zmin,zma (A): -29.09600 33.56100 x,y,z range (A): 55.18900 70.61401 62.65700 scale (grids/A): 2.268672 object centre (A): 35.04150 6.347001 2.232501 number of atom coordinates read : 5142 total number of charged atoms : 4981 net assigned charge : 0.5000154 assigned positive charge : 773.4487 centred at (gu) : 88.55488 86.58903 85.29018 assigned negative charge : -772.9541 centred at (gu) : 88.35129 86.55131 85.28442 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 218753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42035 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98774 mr = 162757 m= 24370 mr = 77545 m= 3087 mr = 17719 m= 112 mr = 1829 m= 0 mr = 11 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 2870 time to turn everything in is 1.900000 number of dielectric boundary points 85235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 39727 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) : 1.512448 object centre at (A) : 35.04150 6.347001 2.232501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5611210E-02 -0.2046341 midg,1,midg; midg,igrid,midg 0.4586766 -5.0944127E-02 1,midg,midg; igrid,midg,midg 3.4249023E-02 5.6488197E-02 gauss-seidel spectral radius is 0.9991591 estimated iterations to convergence 272 setup time was (sec) 2.310000 now iterating at: 16:05:08 rms-change max change #iterations 10.54591 267.5976 at 10iterations 6.067056 165.0624 at 20iterations 3.453559 75.65602 at 30iterations 1.957190 43.50260 at 40iterations 1.104845 24.34922 at 50iterations 0.6213308 11.78672 at 60iterations 0.3485039 6.764610 at 70iterations 0.1956589 3.688501 at 80iterations 0.1092593 2.515233 at 90iterations 6.1128829E-02 1.098653 at 100iterations 3.4130786E-02 0.6338310 at 110iterations 1.9107491E-02 0.3460288 at 120iterations 1.0772832E-02 0.1867085 at 130iterations 6.1524245E-03 0.1151676 at 140iterations 3.5892916E-03 6.6864014E-02 at 150iterations 2.1967583E-03 4.2732239E-02 at 160iterations 1.4289523E-03 2.7724743E-02 at 170iterations 9.9548209E-04 1.7345428E-02 at 180iterations finished qdiffx linear iterations at : 16:05:25 total time elapsed so far: 18.87000 # loops : 180 mean,max change (kT/e) : 9.9548209E-04 1.7345428E-02 energy calculations done at 18.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.04000 DelPhi exited at 16:05:25 19.043u 0.455s 0:19.85 98.1% 0+0k 0+0io 0pf+0w