Sat Oct 15 14:45:00 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 15 2011 at 14:45:00 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! 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: 0.5517413 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): -30.13500 34.38800 ymin,ymax (A): -26.88000 21.32600 zmin,zma (A): -40.80000 7.601000 x,y,z range (A): 64.52299 48.20600 48.40100 scale (grids/A): 0.5517413 object centre (A): 2.126498 -2.776999 -16.59950 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -3.485966 assigned positive charge : 443.7630 centred at (gu) : 90.42854 90.17666 90.56680 assigned negative charge : -447.2501 centred at (gu) : 90.48717 90.31998 90.63693 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5905 nv = 96 ne = 84 npr = 58868 no. pairs analyzed = 58868 no. exposed pairs = 3954 no. arc points = 27979 no. surface atoms = 1329 nbur = 1621 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 = 1.568000 m= 216 mr = 2931 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7082928E-10 -9.7432984E-10 midg,1,midg; midg,igrid,midg 8.6383223E-10 -1.5348584E-09 1,midg,midg; igrid,midg,midg 1.9644769E-10 -8.3388141E-10 gauss-seidel spectral radius is 0.9830635 estimated iterations to convergence 63 setup time was (sec) 0.6200000 now iterating at: 14:45:01 rms-change max change #iterations 7.6510221E-02 19.71170 at 10iterations 5.0900010E-03 1.092010 at 20iterations 3.5246860E-04 6.1920166E-02 at 30iterations 2.4675419E-05 4.0187836E-03 at 40iterations 1.7017106E-06 2.7465820E-04 at 50iterations finished qdiffx linear iterations at : 14:45:06 total time elapsed so far: 5.620000 # loops : 50 mean,max change (kT/e) : 1.7017106E-06 2.7465820E-04 energy calculations done at 5.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.780000 DelPhi exited at 14:45:08 5.789u 0.468s 0:07.60 82.1% 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 Sat Oct 15 2011 at 14:45:08 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! 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: 1.655224 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): -30.13500 34.38800 ymin,ymax (A): -26.88000 21.32600 zmin,zma (A): -40.80000 7.601000 x,y,z range (A): 64.52299 48.20600 48.40100 scale (grids/A): 1.655224 object centre (A): 2.126498 -2.776999 -16.59950 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -3.485966 assigned positive charge : 443.7630 centred at (gu) : 91.28469 90.52918 91.69956 assigned negative charge : -447.2501 centred at (gu) : 91.46107 90.95941 91.91048 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27979 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19098 mr = 42792 m= 1756 mr = 12618 m= 56 mr = 782 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 503 time to turn everything in is 0.5300000 number of dielectric boundary points 29717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21591 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) : 0.5517413 object centre at (A) : 2.126498 -2.776999 -16.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0401428E-04 -4.5006857E-03 midg,1,midg; midg,igrid,midg 8.3552813E-03 -1.8422149E-02 1,midg,midg; igrid,midg,midg 1.1761658E-03 -3.0081259E-02 gauss-seidel spectral radius is 0.9982380 estimated iterations to convergence 189 setup time was (sec) 0.8900000 now iterating at: 14:45:10 rms-change max change #iterations 3.423588 150.6544 at 10iterations 1.440323 60.13654 at 20iterations 0.6053100 23.00915 at 30iterations 0.2558269 10.50483 at 40iterations 0.1078134 3.664871 at 50iterations 4.5520995E-02 1.535595 at 60iterations 1.9089632E-02 0.7656202 at 70iterations 8.0862148E-03 0.3148804 at 80iterations 3.4077915E-03 0.1445923 at 90iterations 1.4400628E-03 5.0662994E-02 at 100iterations 6.0729322E-04 2.1320343E-02 at 110iterations 2.5720708E-04 9.5119476E-03 at 120iterations finished qdiffx linear iterations at : 14:45:28 total time elapsed so far: 13.79000 # loops : 120 mean,max change (kT/e) : 2.5720708E-04 9.5119476E-03 energy calculations done at 13.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 14:45:28 13.958u 0.546s 0:20.19 71.7% 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 Sat Oct 15 2011 at 14:45:28 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! 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: 2.482836 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): -30.13500 34.38800 ymin,ymax (A): -26.88000 21.32600 zmin,zma (A): -40.80000 7.601000 x,y,z range (A): 64.52299 48.20600 48.40100 scale (grids/A): 2.482836 object centre (A): 2.126498 -2.776999 -16.59950 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -3.485966 assigned positive charge : 443.7630 centred at (gu) : 91.92692 90.79378 92.54922 assigned negative charge : -447.2501 centred at (gu) : 92.19161 91.43912 92.86562 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 150741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27979 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 66741 mr = 104897 m= 17996 mr = 51653 m= 2697 mr = 13077 m= 187 mr = 1571 m= 3 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 1665 time to turn everything in is 1.330000 number of dielectric boundary points 67064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 22456 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) : 1.655224 object centre at (A) : 2.126498 -2.776999 -16.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5812676E-02 -3.1420797E-02 midg,1,midg; midg,igrid,midg 0.1307978 -0.2491562 1,midg,midg; igrid,midg,midg 0.3644412 -0.7788828 gauss-seidel spectral radius is 0.9991611 estimated iterations to convergence 273 setup time was (sec) 1.740000 now iterating at: 14:45:33 rms-change max change #iterations 8.815503 324.1531 at 10iterations 4.960098 149.6343 at 20iterations 2.782801 73.63815 at 30iterations 1.556111 40.11841 at 40iterations 0.8661144 20.44392 at 50iterations 0.4840824 9.523141 at 60iterations 0.2687375 5.746086 at 70iterations 0.1491602 3.134829 at 80iterations 8.2730353E-02 1.999886 at 90iterations 4.5771144E-02 0.9235001 at 100iterations 2.5436915E-02 0.5638142 at 110iterations 1.4038353E-02 0.2968235 at 120iterations 7.7696498E-03 0.1696930 at 130iterations 4.3025035E-03 9.1731071E-02 at 140iterations 2.3765864E-03 4.8957825E-02 at 150iterations 1.3151136E-03 2.7851105E-02 at 160iterations 7.2894047E-04 1.4891624E-02 at 170iterations 4.0340988E-04 8.7261200E-03 at 180iterations finished qdiffx linear iterations at : 14:46:04 total time elapsed so far: 22.47000 # loops : 180 mean,max change (kT/e) : 4.0340988E-04 8.7261200E-03 energy calculations done at 22.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.65000 DelPhi exited at 14:46:05 22.658u 0.547s 0:36.66 63.2% 0+0k 0+0io 0pf+0w