Mon Oct 10 17:01:40 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 Mon Oct 10 2011 at 17:01:40 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 = 2759 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: 0.5681275 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 0.5681275 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5000247 assigned positive charge : 413.7165 centred at (gu) : 90.41641 88.95004 89.80363 assigned negative charge : -413.2173 centred at (gu) : 90.29507 88.75273 89.63596 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5995 nv = 96 ne = 84 npr = 54275 no. pairs analyzed = 54275 no. exposed pairs = 3630 no. arc points = 25591 no. surface atoms = 1217 nbur = 1542 mkacc time = 9.0000004E-02 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 = 1.512000 m= 227 mr = 3020 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.1900000 number of dielectric boundary points 3193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2579 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3428084E-09 2.2443845E-09 midg,1,midg; midg,igrid,midg -3.4368857E-09 2.1288284E-09 1,midg,midg; igrid,midg,midg -1.4253151E-09 1.9274553E-09 gauss-seidel spectral radius is 0.9840032 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 17:01:41 rms-change max change #iterations 8.5601583E-02 18.71562 at 10iterations 6.3380511E-03 1.118448 at 20iterations 4.6953614E-04 7.0615768E-02 at 30iterations 3.4655732E-05 6.3705444E-03 at 40iterations 2.5606523E-06 4.1198730E-04 at 50iterations finished qdiffx linear iterations at : 17:01:44 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.5606523E-06 4.1198730E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:01:45 3.378u 0.172s 0:04.27 82.9% 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 Mon Oct 10 2011 at 17:01:45 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 = 2759 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: 1.704382 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 1.704382 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5000247 assigned positive charge : 413.7165 centred at (gu) : 91.24826 86.84924 89.41013 assigned negative charge : -413.2173 centred at (gu) : 90.88496 86.25813 88.90729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25591 grid for indexing accessible points = 1.400000 m= 20412 mr = 43691 m= 2228 mr = 13792 m= 74 mr = 1083 m= 0 mr = 15 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2164 time to turn everything in is 0.3200000 number of dielectric boundary points 29499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20259 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) : 0.5681275 object centre at (A) : 0.3479996 0.2515001 -23.97750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7723311E-03 7.5738467E-03 midg,1,midg; midg,igrid,midg -2.8706709E-02 8.7862369E-03 1,midg,midg; igrid,midg,midg -9.9413982E-03 2.7834186E-02 gauss-seidel spectral radius is 0.9983226 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 17:01:45 rms-change max change #iterations 3.507077 182.9213 at 10iterations 1.506624 63.73794 at 20iterations 0.6469954 24.22025 at 30iterations 0.2792881 9.873796 at 40iterations 0.1200014 4.288666 at 50iterations 5.1637497E-02 1.902285 at 60iterations 2.2307279E-02 0.7282090 at 70iterations 9.5834658E-03 0.3424921 at 80iterations 4.1382564E-03 0.1528778 at 90iterations 1.7877321E-03 6.4758301E-02 at 100iterations 7.6480745E-04 2.8134346E-02 at 110iterations 3.3200413E-04 1.3576508E-02 at 120iterations finished qdiffx linear iterations at : 17:01:53 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 3.3200413E-04 1.3576508E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 17:01:54 8.457u 0.195s 0:08.97 96.3% 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 Mon Oct 10 2011 at 17:01:54 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 = 2759 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: 2.556573 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 2.556573 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5000247 assigned positive charge : 413.7165 centred at (gu) : 91.87206 85.27370 89.11497 assigned negative charge : -413.2173 centred at (gu) : 91.32728 84.38698 88.36092 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 151842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25591 grid for indexing accessible points = 1.400000 m= 69563 mr = 107053 m= 20510 mr = 54484 m= 3524 mr = 15282 m= 290 mr = 2266 m= 9 mr = 125 m= 0 mr = 5 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6910 time to turn everything in is 0.7700000 number of dielectric boundary points 66523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20944 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) : 1.704382 object centre at (A) : 0.3479996 0.2515001 -23.97750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2698744E-02 8.9037567E-02 midg,1,midg; midg,igrid,midg -0.3775049 0.1321650 1,midg,midg; igrid,midg,midg 0.2314331 0.3033570 gauss-seidel spectral radius is 0.9991810 estimated iterations to convergence 276 setup time was (sec) 1.010000 now iterating at: 17:01:55 rms-change max change #iterations 8.912426 283.5093 at 10iterations 5.071101 125.4176 at 20iterations 2.865563 67.56972 at 30iterations 1.615471 35.33549 at 40iterations 0.9070643 19.41228 at 50iterations 0.5081662 11.16621 at 60iterations 0.2855124 5.944392 at 70iterations 0.1589980 3.530969 at 80iterations 8.9081287E-02 1.757763 at 90iterations 4.9723838E-02 0.9879036 at 100iterations 2.7788403E-02 0.6441067 at 110iterations 1.5471905E-02 0.2972189 at 120iterations 8.6291777E-03 0.1613541 at 130iterations 4.8080897E-03 9.9604130E-02 at 140iterations 2.6770241E-03 5.4160118E-02 at 150iterations 1.4912669E-03 2.9262543E-02 at 160iterations 8.3266705E-04 1.7446518E-02 at 170iterations 4.6341127E-04 9.2468262E-03 at 180iterations finished qdiffx linear iterations at : 17:02:06 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 4.6341127E-04 9.2468262E-03 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 17:02:07 12.455u 0.225s 0:13.02 97.3% 0+0k 0+0io 0pf+0w