Sat Oct 8 11:41:26 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 Sat Oct 8 2011 at 11:41:26 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6110853 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 0.6110853 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999991 assigned positive charge : 372.0657 centred at (gu) : 93.72010 89.60036 90.12987 assigned negative charge : -374.0663 centred at (gu) : 93.63492 89.54012 90.15029 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6312 nv = 96 ne = 84 npr = 51958 no. pairs analyzed = 51958 no. exposed pairs = 3228 no. arc points = 23058 no. surface atoms = 1098 nbur = 1453 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3287 m= 3 mr = 20 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 0.1900000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2337 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7764 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6019004E-10 -2.4179936E-09 midg,1,midg; midg,igrid,midg -4.7011026E-09 1.4047942E-09 1,midg,midg; igrid,midg,midg -2.4386659E-09 6.6218129E-09 gauss-seidel spectral radius is 0.9861354 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 11:41:27 rms-change max change #iterations 0.1200584 17.87169 at 10iterations 1.0540391E-02 1.665068 at 20iterations 9.4109942E-04 0.1728401 at 30iterations 8.4266088E-05 1.3931274E-02 at 40iterations 8.5114762E-06 1.4553070E-03 at 50iterations finished qdiffx linear iterations at : 11:41:30 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.5114762E-06 1.4553070E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 11:41:30 3.362u 0.173s 0:03.85 91.6% 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 Sat Oct 8 2011 at 11:41:30 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.833256 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 1.833256 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999991 assigned positive charge : 372.0657 centred at (gu) : 101.1594 88.80051 90.38914 assigned negative charge : -374.0663 centred at (gu) : 100.9045 88.62007 90.45058 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23058 grid for indexing accessible points = 1.400000 m= 23226 mr = 45563 m= 3301 mr = 16758 m= 128 mr = 1931 m= 2 mr = 31 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 0.3400000 number of dielectric boundary points 30427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18790 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) : 0.6110853 object centre at (A) : 46.83550 29.22550 38.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0604832E-02 -2.2677857E-02 midg,1,midg; midg,igrid,midg 8.2918396E-03 -3.9192077E-04 1,midg,midg; igrid,midg,midg -1.2962469E-02 3.3753503E-02 gauss-seidel spectral radius is 0.9985175 estimated iterations to convergence 206 setup time was (sec) 0.5500000 now iterating at: 11:41:31 rms-change max change #iterations 3.840442 220.7432 at 10iterations 1.737727 75.44404 at 20iterations 0.7858573 25.81120 at 30iterations 0.3559026 11.70668 at 40iterations 0.1615261 5.102137 at 50iterations 7.3397361E-02 2.352551 at 60iterations 3.3241082E-02 1.086382 at 70iterations 1.5031124E-02 0.5027351 at 80iterations 6.8242932E-03 0.2296333 at 90iterations 3.0913712E-03 0.1005745 at 100iterations 1.4061745E-03 4.6747208E-02 at 110iterations 6.3802651E-04 2.1955490E-02 at 120iterations finished qdiffx linear iterations at : 11:41:38 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 6.3802651E-04 2.1955490E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 11:41:39 7.698u 0.211s 0:08.33 94.8% 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 8 2011 at 11:41:39 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.749884 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 2.749884 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999991 assigned positive charge : 372.0657 centred at (gu) : 106.7391 88.20074 90.58347 assigned negative charge : -374.0663 centred at (gu) : 106.3566 87.92995 90.67590 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23058 grid for indexing accessible points = 1.400000 m= 75978 mr = 110850 m= 26611 mr = 61078 m= 5698 mr = 21043 m= 626 mr = 4164 m= 28 mr = 359 m= 0 mr = 3 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 68618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19220 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) : 1.833256 object centre at (A) : 46.83550 29.22550 38.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1408815 -0.2864280 midg,1,midg; midg,igrid,midg 0.2201977 1.5851039E-02 1,midg,midg; igrid,midg,midg -7.3190354E-02 0.5494136 gauss-seidel spectral radius is 0.9992316 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 11:41:40 rms-change max change #iterations 9.246453 299.7504 at 10iterations 5.362243 130.9873 at 20iterations 3.098106 67.12688 at 30iterations 1.779062 36.54121 at 40iterations 1.018965 21.46038 at 50iterations 0.5809969 13.72352 at 60iterations 0.3318403 6.656893 at 70iterations 0.1894126 3.724075 at 80iterations 0.1076698 2.014001 at 90iterations 6.1315149E-02 1.172629 at 100iterations 3.4860514E-02 0.6497431 at 110iterations 1.9845430E-02 0.3851147 at 120iterations 1.1291876E-02 0.2167511 at 130iterations 6.4252834E-03 0.1240425 at 140iterations 3.6575790E-03 7.2689265E-02 at 150iterations 2.0833055E-03 4.3247223E-02 at 160iterations 1.1872198E-03 2.4267197E-02 at 170iterations 6.7956932E-04 1.2987137E-02 at 180iterations finished qdiffx linear iterations at : 11:41:51 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 6.7956932E-04 1.2987137E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 11:41:52 12.465u 0.218s 0:13.03 97.2% 0+0k 0+0io 0pf+0w