Mon Oct 10 19:49:01 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 19:49:01 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 = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5017194 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): -3.127000 67.82899 ymin,ymax (A): -12.56300 38.86200 zmin,zma (A): -20.00000 45.16200 x,y,z range (A): 70.95599 51.42500 65.16200 scale (grids/A): 0.5017194 object centre (A): 32.35100 13.14950 12.58100 number of atom coordinates read : 4403 total number of charged atoms : 4248 net assigned charge : -5.499951 assigned positive charge : 665.1478 centred at (gu) : 88.14378 89.99714 90.80865 assigned negative charge : -670.6501 centred at (gu) : 88.19941 90.11748 90.81249 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6874 nv = 96 ne = 84 npr = 91785 no. pairs analyzed = 91785 no. exposed pairs = 5086 no. arc points = 34186 no. surface atoms = 1733 nbur = 2670 mkacc time = 0.2100000 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= 225 mr = 3771 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3419 ## 536 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9339 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8396012E-11 -7.4156022E-11 midg,1,midg; midg,igrid,midg 1.4153925E-10 -2.5495805E-10 1,midg,midg; igrid,midg,midg 6.4106463E-11 -8.9272749E-11 gauss-seidel spectral radius is 0.9796508 estimated iterations to convergence 58 setup time was (sec) 0.6800000 now iterating at: 19:49:02 rms-change max change #iterations 5.8861248E-02 12.72471 at 10iterations 3.3876635E-03 0.6544876 at 20iterations 3.7583313E-04 5.1160812E-02 at 30iterations 9.1688293E-05 1.1980057E-02 at 40iterations 2.5343186E-05 3.1163692E-03 at 50iterations finished qdiffx linear iterations at : 19:49:05 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 2.5343186E-05 3.1163692E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 19:49:06 4.256u 0.260s 0:04.83 93.3% 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 Mon Oct 10 2011 at 19:49:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.505158 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): -3.127000 67.82899 ymin,ymax (A): -12.56300 38.86200 zmin,zma (A): -20.00000 45.16200 x,y,z range (A): 70.95599 51.42500 65.16200 scale (grids/A): 1.505158 object centre (A): 32.35100 13.14950 12.58100 number of atom coordinates read : 4403 total number of charged atoms : 4248 net assigned charge : -5.499951 assigned positive charge : 665.1478 centred at (gu) : 84.43008 89.99020 92.42493 assigned negative charge : -670.6501 centred at (gu) : 84.59777 90.35183 92.43707 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34186 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23081 mr = 56511 m= 1903 mr = 15834 m= 22 mr = 764 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.6600000 number of dielectric boundary points 31020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 498 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 31809 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) : 0.5017194 object centre at (A) : 32.35100 13.14950 12.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1122499E-03 -8.3519323E-03 midg,1,midg; midg,igrid,midg 2.3112784E-03 -9.7173853E-03 1,midg,midg; igrid,midg,midg 1.2926003E-02 -3.3239510E-03 gauss-seidel spectral radius is 0.9979776 estimated iterations to convergence 177 setup time was (sec) 1.010000 now iterating at: 19:49:07 rms-change max change #iterations 3.463355 138.3377 at 10iterations 1.370670 51.18946 at 20iterations 0.5469696 20.17958 at 30iterations 0.2177792 7.208069 at 40iterations 8.6754896E-02 2.881184 at 50iterations 3.4610186E-02 1.174764 at 60iterations 1.3882363E-02 0.4690208 at 70iterations 5.6041260E-03 0.1890717 at 80iterations 2.3064245E-03 8.1020355E-02 at 90iterations 9.9182792E-04 3.3458710E-02 at 100iterations 4.6123101E-04 1.6918421E-02 at 110iterations 2.3895595E-04 7.9841614E-03 at 120iterations finished qdiffx linear iterations at : 19:49:15 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 2.3895595E-04 7.9841614E-03 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 19:49:16 9.723u 0.269s 0:10.44 95.5% 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 19:49:16 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 = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.257737 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): -3.127000 67.82899 ymin,ymax (A): -12.56300 38.86200 zmin,zma (A): -20.00000 45.16200 x,y,z range (A): 70.95599 51.42500 65.16200 scale (grids/A): 2.257737 object centre (A): 32.35100 13.14950 12.58100 number of atom coordinates read : 4403 total number of charged atoms : 4248 net assigned charge : -5.499951 assigned positive charge : 665.1478 centred at (gu) : 81.64494 89.98495 93.63721 assigned negative charge : -670.6501 centred at (gu) : 81.89654 90.52766 93.65544 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 184757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34186 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 83943 mr = 138566 m= 20772 mr = 66918 m= 2562 mr = 15158 m= 85 mr = 1556 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2087 time to turn everything in is 1.500000 number of dielectric boundary points 69911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 33874 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) : 1.505158 object centre at (A) : 32.35100 13.14950 12.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1889892 -0.1879782 midg,1,midg; midg,igrid,midg 2.6861835E-02 -0.1595998 1,midg,midg; igrid,midg,midg 0.3218335 -0.4269212 gauss-seidel spectral radius is 0.9990984 estimated iterations to convergence 263 setup time was (sec) 1.840000 now iterating at: 19:49:18 rms-change max change #iterations 9.490095 335.3015 at 10iterations 5.297776 118.8386 at 20iterations 2.934321 66.20176 at 30iterations 1.622264 37.70702 at 40iterations 0.8873894 19.17086 at 50iterations 0.4867614 9.534626 at 60iterations 0.2660535 5.586761 at 70iterations 0.1451788 2.874664 at 80iterations 7.9169914E-02 1.517201 at 90iterations 4.3066803E-02 0.8118610 at 100iterations 2.3435563E-02 0.4739275 at 110iterations 1.2755577E-02 0.2411146 at 120iterations 6.9466722E-03 0.1371659 at 130iterations 3.7699987E-03 7.4597359E-02 at 140iterations 2.0539290E-03 3.9674759E-02 at 150iterations 1.1223266E-03 2.4204254E-02 at 160iterations 6.1468431E-04 1.1701584E-02 at 170iterations 3.3996350E-04 6.9408417E-03 at 180iterations finished qdiffx linear iterations at : 19:49:32 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 3.3996350E-04 6.9408417E-03 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.55000 DelPhi exited at 19:49:32 15.548u 0.282s 0:16.10 98.2% 0+0k 0+0io 0pf+0w