Sat Oct 15 12:32:46 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 15 2011 at 12:32:46 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5447423 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 0.5447423 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 406.6866 centred at (gu) : 90.45390 89.64492 88.88080 assigned negative charge : -422.9100 centred at (gu) : 90.18330 89.72552 88.72842 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5281 nv = 96 ne = 84 npr = 56718 no. pairs analyzed = 56718 no. exposed pairs = 3682 no. arc points = 25643 no. surface atoms = 1232 nbur = 1517 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= 174 mr = 2552 m= 0 mr = 8 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 2895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4986520E-09 -5.1077136E-11 midg,1,midg; midg,igrid,midg -5.1565857E-10 -1.3268843E-09 1,midg,midg; igrid,midg,midg -2.3630662E-09 7.0123413E-10 gauss-seidel spectral radius is 0.9826115 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 12:32:47 rms-change max change #iterations 6.8353213E-02 12.33293 at 10iterations 4.4375509E-03 0.9101372 at 20iterations 3.6807387E-04 5.3741455E-02 at 30iterations 6.8490073E-05 9.5868111E-03 at 40iterations 1.8898319E-05 2.4795532E-03 at 50iterations finished qdiffx linear iterations at : 12:32:52 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 1.8898319E-05 2.4795532E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.180000 DelPhi exited at 12:32:52 5.184u 0.469s 0:05.92 95.2% 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 15 2011 at 12:32:52 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.634227 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 1.634227 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 406.6866 centred at (gu) : 91.36113 88.93407 86.64206 assigned negative charge : -422.9100 centred at (gu) : 90.54949 89.17639 86.18468 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17109 mr = 38422 m= 1445 mr = 11462 m= 24 mr = 576 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.5000000 number of dielectric boundary points 26623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19684 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) : 0.5447423 object centre at (A) : 4.056000 49.02000 18.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1809679E-02 -3.3889671E-03 midg,1,midg; midg,igrid,midg -1.6115239E-02 -5.5040501E-02 1,midg,midg; igrid,midg,midg -2.0474108E-02 4.4289255E-03 gauss-seidel spectral radius is 0.9981570 estimated iterations to convergence 185 setup time was (sec) 0.8400000 now iterating at: 12:32:54 rms-change max change #iterations 3.197558 171.9482 at 10iterations 1.326759 55.63430 at 20iterations 0.5497164 21.40719 at 30iterations 0.2268568 9.109037 at 40iterations 9.4045356E-02 3.749405 at 50iterations 3.8960803E-02 1.503742 at 60iterations 1.6107611E-02 0.6659536 at 70iterations 6.6825645E-03 0.2516899 at 80iterations 2.7768956E-03 0.1107426 at 90iterations 1.1654053E-03 4.0993333E-02 at 100iterations 4.9139030E-04 1.7177582E-02 at 110iterations 2.1418033E-04 7.7838898E-03 at 120iterations finished qdiffx linear iterations at : 12:33:05 total time elapsed so far: 11.78000 # loops : 120 mean,max change (kT/e) : 2.1418033E-04 7.7838898E-03 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 12:33:05 11.966u 0.519s 0:12.84 97.1% 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 12:33:05 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.451340 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 2.451340 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 406.6866 centred at (gu) : 92.04153 88.40098 84.96268 assigned negative charge : -422.9100 centred at (gu) : 90.82414 88.76456 84.27695 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 135410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 60259 mr = 94011 m= 15790 mr = 46920 m= 2132 mr = 11472 m= 118 mr = 1271 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7199999 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 1.220000 number of dielectric boundary points 59984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 20488 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) : 1.634227 object centre at (A) : 4.056000 49.02000 18.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2858093 -4.1191753E-02 midg,1,midg; midg,igrid,midg -0.2160657 -0.7796799 1,midg,midg; igrid,midg,midg -0.2851985 7.5892329E-02 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.580000 now iterating at: 12:33:07 rms-change max change #iterations 8.433171 311.2357 at 10iterations 4.747456 131.2425 at 20iterations 2.666408 68.26984 at 30iterations 1.491784 38.57154 at 40iterations 0.8297404 21.52715 at 50iterations 0.4612978 11.94690 at 60iterations 0.2557682 5.996358 at 70iterations 0.1414374 3.406403 at 80iterations 7.8108646E-02 1.836723 at 90iterations 4.3079261E-02 0.9961838 at 100iterations 2.3730377E-02 0.6076086 at 110iterations 1.3067354E-02 0.3124199 at 120iterations 7.1917824E-03 0.1668015 at 130iterations 3.9591743E-03 0.1117323 at 140iterations 2.1797754E-03 5.5558681E-02 at 150iterations 1.2004813E-03 2.6937485E-02 at 160iterations 6.6343741E-04 1.4564514E-02 at 170iterations 3.6854731E-04 8.7738037E-03 at 180iterations finished qdiffx linear iterations at : 12:33:25 total time elapsed so far: 19.54000 # loops : 180 mean,max change (kT/e) : 3.6854731E-04 8.7738037E-03 energy calculations done at 19.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.70000 DelPhi exited at 12:33:26 19.706u 0.587s 0:20.55 98.6% 0+0k 0+0io 0pf+0w