Sat Oct 8 11:39:02 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 Sat Oct 8 2011 at 11:39:02 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 = 2923 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: 0.5365162 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 0.5365162 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.999990 assigned positive charge : 430.0550 centred at (gu) : 88.91294 88.52419 90.23628 assigned negative charge : -440.0560 centred at (gu) : 88.98050 88.64836 90.28340 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5505 nv = 96 ne = 84 npr = 58091 no. pairs analyzed = 58091 no. exposed pairs = 3988 no. arc points = 28446 no. surface atoms = 1347 nbur = 1576 mkacc time = 0.1700000 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= 226 mr = 2662 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1139633E-10 -6.9404571E-10 midg,1,midg; midg,igrid,midg 1.8848678E-10 -7.0286915E-10 1,midg,midg; igrid,midg,midg -1.6645157E-10 -5.7249266E-10 gauss-seidel spectral radius is 0.9821005 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 11:39:02 rms-change max change #iterations 6.1677616E-02 12.41790 at 10iterations 3.9938125E-03 0.6766024 at 20iterations 2.5832586E-04 4.6092987E-02 at 30iterations 1.9693965E-05 3.6201477E-03 at 40iterations 2.4549038E-06 5.4407120E-04 at 50iterations finished qdiffx linear iterations at : 11:39:06 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.4549038E-06 5.4407120E-04 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 11:39:06 4.093u 0.157s 0:04.60 92.1% 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 8 2011 at 11:39:06 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 = 2923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.609549 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 1.609549 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.999990 assigned positive charge : 430.0550 centred at (gu) : 86.73773 85.57146 90.70797 assigned negative charge : -440.0560 centred at (gu) : 86.94116 85.94467 90.84965 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17352 mr = 39541 m= 1563 mr = 11246 m= 38 mr = 623 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 28569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21093 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) : 0.5365162 object centre at (A) : 19.99900 5.504000 6.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3978267E-03 -7.9943202E-03 midg,1,midg; midg,igrid,midg -1.3026397E-04 -1.7663185E-02 1,midg,midg; igrid,midg,midg 1.4987044E-03 -8.5087493E-03 gauss-seidel spectral radius is 0.9981315 estimated iterations to convergence 184 setup time was (sec) 0.9200000 now iterating at: 11:39:07 rms-change max change #iterations 3.185159 149.7275 at 10iterations 1.302678 53.81026 at 20iterations 0.5367843 20.57574 at 30iterations 0.2194648 8.055134 at 40iterations 9.0191908E-02 3.389759 at 50iterations 3.7291117E-02 1.484729 at 60iterations 1.5297118E-02 0.6151505 at 70iterations 6.2964018E-03 0.2187653 at 80iterations 2.5927038E-03 0.1038389 at 90iterations 1.0674411E-03 5.0872803E-02 at 100iterations 4.3862936E-04 1.5783310E-02 at 110iterations 1.8096443E-04 7.2531700E-03 at 120iterations finished qdiffx linear iterations at : 11:39:16 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 1.8096443E-04 7.2531700E-03 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 11:39:17 9.848u 0.214s 0:10.36 97.0% 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 11:39:17 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 = 2923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.414323 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 2.414323 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.999990 assigned positive charge : 430.0550 centred at (gu) : 85.10655 83.35719 91.06157 assigned negative charge : -440.0560 centred at (gu) : 85.41156 83.91691 91.27439 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 141821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 60967 mr = 97507 m= 15937 mr = 46664 m= 2219 mr = 11254 m= 137 mr = 1235 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 64352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 22088 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) : 1.609549 object centre at (A) : 19.99900 5.504000 6.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1026052E-02 -0.1040890 midg,1,midg; midg,igrid,midg 0.3354311 -0.2519801 1,midg,midg; igrid,midg,midg 3.0448023E-02 -0.1167644 gauss-seidel spectral radius is 0.9991220 estimated iterations to convergence 267 setup time was (sec) 1.710000 now iterating at: 11:39:19 rms-change max change #iterations 8.444027 281.2103 at 10iterations 4.753340 137.7494 at 20iterations 2.658786 97.11813 at 30iterations 1.475464 33.68365 at 40iterations 0.8144298 21.77907 at 50iterations 0.4496975 10.34459 at 60iterations 0.2479903 6.462268 at 70iterations 0.1361973 3.377073 at 80iterations 7.4645489E-02 1.568847 at 90iterations 4.0922083E-02 0.9349823 at 100iterations 2.2383226E-02 0.4952774 at 110iterations 1.2236747E-02 0.2720184 at 120iterations 6.7080352E-03 0.1543736 at 130iterations 3.6632700E-03 7.8475952E-02 at 140iterations 2.0047580E-03 4.4842958E-02 at 150iterations 1.0983449E-03 2.4791718E-02 at 160iterations 6.0168229E-04 1.2404608E-02 at 170iterations 3.2960708E-04 7.3647499E-03 at 180iterations finished qdiffx linear iterations at : 11:39:31 total time elapsed so far: 14.06000 # loops : 180 mean,max change (kT/e) : 3.2960708E-04 7.3647499E-03 energy calculations done at 14.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 11:39:31 14.286u 0.210s 0:14.77 98.1% 0+0k 0+0io 0pf+0w