Sat Oct 8 17:16:07 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 17:16:07 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 0.5548629 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 0.5548629 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 506.3185 centred at (gu) : 89.93487 90.08564 89.62294 assigned negative charge : -512.8198 centred at (gu) : 89.94992 90.06405 89.59926 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 67460 no. pairs analyzed = 67460 no. exposed pairs = 4220 no. arc points = 29082 no. surface atoms = 1422 nbur = 1944 mkacc time = 0.1500000 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= 302 mr = 3692 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0034974E-10 -2.9228089E-10 midg,1,midg; midg,igrid,midg -7.8365697E-10 -3.4720329E-10 1,midg,midg; igrid,midg,midg -4.1596779E-10 -7.1874812E-10 gauss-seidel spectral radius is 0.9832776 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 17:16:08 rms-change max change #iterations 8.5942864E-02 12.38771 at 10iterations 6.0876203E-03 0.9673491 at 20iterations 4.9236719E-04 8.0895424E-02 at 30iterations 6.4265732E-05 1.4337540E-02 at 40iterations 1.3934286E-05 3.0794144E-03 at 50iterations finished qdiffx linear iterations at : 17:16:10 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.3934286E-05 3.0794144E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:16:11 3.235u 0.139s 0:03.65 92.0% 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 17:16:11 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.664589 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 1.664589 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 506.3185 centred at (gu) : 89.80376 90.25594 88.86791 assigned negative charge : -512.8198 centred at (gu) : 89.84937 90.19176 88.79723 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29082 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25034 mr = 52402 m= 2973 mr = 17803 m= 105 mr = 1605 m= 0 mr = 14 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 31589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 24727 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) : 0.5548629 object centre at (A) : 66.09950 48.78400 2.004001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0177886E-03 -4.6599004E-03 midg,1,midg; midg,igrid,midg 7.2622956E-03 1.7202936E-02 1,midg,midg; igrid,midg,midg -1.7720856E-02 -9.3353530E-03 gauss-seidel spectral radius is 0.9982954 estimated iterations to convergence 192 setup time was (sec) 0.7800000 now iterating at: 17:16:12 rms-change max change #iterations 3.746650 172.7330 at 10iterations 1.599483 60.95584 at 20iterations 0.6862521 23.34453 at 30iterations 0.2943015 11.16907 at 40iterations 0.1264724 4.445271 at 50iterations 5.4105606E-02 1.835018 at 60iterations 2.3309160E-02 0.7972202 at 70iterations 9.9812290E-03 0.3424311 at 80iterations 4.3107313E-03 0.1435471 at 90iterations 1.8599706E-03 5.9142113E-02 at 100iterations 8.0425490E-04 2.5746346E-02 at 110iterations 3.5487022E-04 1.2269974E-02 at 120iterations finished qdiffx linear iterations at : 17:16:18 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 3.5487022E-04 1.2269974E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 17:16:19 7.196u 0.200s 0:07.68 96.2% 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 17:16:19 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 2.496883 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 2.496883 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 506.3185 centred at (gu) : 89.70538 90.38361 88.30173 assigned negative charge : -512.8198 centred at (gu) : 89.77389 90.28753 88.19581 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 174820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29082 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84860 mr = 127762 m= 26096 mr = 68356 m= 4846 mr = 20142 m= 430 mr = 3272 m= 10 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 71290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 25742 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) : 1.664589 object centre at (A) : 66.09950 48.78400 2.004001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7495742E-02 -4.8745602E-02 midg,1,midg; midg,igrid,midg 0.2623182 0.5342370 1,midg,midg; igrid,midg,midg -0.2743594 -0.1089041 gauss-seidel spectral radius is 0.9991806 estimated iterations to convergence 276 setup time was (sec) 1.560000 now iterating at: 17:16:20 rms-change max change #iterations 9.561073 255.9761 at 10iterations 5.444391 125.2713 at 20iterations 3.078216 61.68818 at 30iterations 1.733492 33.55720 at 40iterations 0.9755605 18.41165 at 50iterations 0.5482488 10.73290 at 60iterations 0.3070106 6.321285 at 70iterations 0.1715670 3.283171 at 80iterations 9.6205443E-02 1.977282 at 90iterations 5.3728994E-02 1.157211 at 100iterations 3.0007850E-02 0.5951691 at 110iterations 1.6797239E-02 0.3144572 at 120iterations 9.3810977E-03 0.1724329 at 130iterations 5.2372152E-03 0.1082826 at 140iterations 2.9334873E-03 5.6599617E-02 at 150iterations 1.6462922E-03 3.0268669E-02 at 160iterations 9.2908472E-04 1.9001961E-02 at 170iterations 5.2799785E-04 1.0053635E-02 at 180iterations finished qdiffx linear iterations at : 17:16:30 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 5.2799785E-04 1.0053635E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 17:16:30 11.362u 0.202s 0:11.85 97.5% 0+0k 0+0io 0pf+0w