Mon Oct 10 14:10:00 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+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 14:10:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 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: 0.5750933 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 0.5750933 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 513.1506 centred at (gu) : 88.40849 91.00871 89.44099 assigned negative charge : -517.1517 centred at (gu) : 88.39024 91.02922 89.44260 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7554 nv = 96 ne = 84 npr = 69434 no. pairs analyzed = 69434 no. exposed pairs = 4094 no. arc points = 28500 no. surface atoms = 1391 nbur = 2028 mkacc time = 0.1800000 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 = 1.484000 m= 329 mr = 4205 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2972 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9623 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7983814E-10 -6.6523309E-10 midg,1,midg; midg,igrid,midg -2.2532093E-10 -1.4770090E-09 1,midg,midg; igrid,midg,midg -1.6231878E-09 -2.3304086E-10 gauss-seidel spectral radius is 0.9844284 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 14:10:01 rms-change max change #iterations 0.1021525 13.50336 at 10iterations 7.7432855E-03 1.022749 at 20iterations 6.3870731E-04 9.2144728E-02 at 30iterations 7.6477161E-05 1.0924339E-02 at 40iterations 1.6532002E-05 2.8457642E-03 at 50iterations finished qdiffx linear iterations at : 14:10:05 total time elapsed so far: 4.870000 # loops : 50 mean,max change (kT/e) : 1.6532002E-05 2.8457642E-03 energy calculations done at 4.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 14:10:06 5.043u 0.426s 0:05.98 91.3% 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 14:10:06 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 = 3419 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: 1.725280 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 1.725280 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 513.1506 centred at (gu) : 85.22437 93.02518 88.32201 assigned negative charge : -517.1517 centred at (gu) : 85.17005 93.08727 88.32747 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28500 grid for indexing accessible points = 1.400000 m= 28476 mr = 58999 m= 3449 mr = 20644 m= 112 mr = 1850 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.6900000 number of dielectric boundary points 33583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 25372 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) : 0.5750933 object centre at (A) : 16.56450 34.67150 27.24150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3753711E-02 -4.8298049E-03 midg,1,midg; midg,igrid,midg -4.8000668E-03 -1.2156298E-02 1,midg,midg; igrid,midg,midg 4.1505214E-04 -4.2906017E-03 gauss-seidel spectral radius is 0.9984144 estimated iterations to convergence 199 setup time was (sec) 1.040000 now iterating at: 14:10:07 rms-change max change #iterations 4.047004 189.8636 at 10iterations 1.785067 58.64907 at 20iterations 0.7903303 25.93307 at 30iterations 0.3488506 10.93808 at 40iterations 0.1536696 4.717696 at 50iterations 6.7849539E-02 2.134450 at 60iterations 2.9968439E-02 0.9494591 at 70iterations 1.3321002E-02 0.4303589 at 80iterations 5.8905566E-03 0.1728516 at 90iterations 2.6135289E-03 7.8500032E-02 at 100iterations 1.1612078E-03 3.3423901E-02 at 110iterations 5.1865057E-04 1.7431259E-02 at 120iterations finished qdiffx linear iterations at : 14:10:19 total time elapsed so far: 12.49000 # loops : 120 mean,max change (kT/e) : 5.1865057E-04 1.7431259E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 14:10:19 12.669u 0.470s 0:13.44 97.6% 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 14:10:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3419 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: 2.587920 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): -10.03000 43.15900 ymin,ymax (A): 6.634000 62.70900 zmin,zma (A): -3.710000 58.19300 x,y,z range (A): 53.18900 56.07500 61.90300 scale (grids/A): 2.587920 object centre (A): 16.56450 34.67150 27.24150 number of atom coordinates read : 3419 total number of charged atoms : 3275 net assigned charge : -3.999993 assigned positive charge : 513.1506 centred at (gu) : 82.83658 94.53738 87.48290 assigned negative charge : -517.1517 centred at (gu) : 82.75500 94.63086 87.49109 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 192958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28500 grid for indexing accessible points = 1.400000 m= 96316 mr = 143535 m= 30230 mr = 78581 m= 5678 mr = 23622 m= 537 mr = 3897 m= 13 mr = 291 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 1.720000 number of dielectric boundary points 75807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 26192 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) : 1.725280 object centre at (A) : 16.56450 34.67150 27.24150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1975608 -7.2994284E-02 midg,1,midg; midg,igrid,midg -4.2211898E-02 -0.1284532 1,midg,midg; igrid,midg,midg -6.9460575E-03 -5.7305093E-03 gauss-seidel spectral radius is 0.9992115 estimated iterations to convergence 281 setup time was (sec) 2.070000 now iterating at: 14:10:22 rms-change max change #iterations 10.06877 262.1357 at 10iterations 5.804128 131.6015 at 20iterations 3.305833 64.54305 at 30iterations 1.887951 36.21702 at 40iterations 1.074027 20.20302 at 50iterations 0.6107417 11.77640 at 60iterations 0.3464049 6.514156 at 70iterations 0.1963747 3.447746 at 80iterations 0.1111154 1.931142 at 90iterations 6.2644444E-02 1.279204 at 100iterations 3.5417031E-02 0.6455231 at 110iterations 2.0016648E-02 0.3568947 at 120iterations 1.1326686E-02 0.1960006 at 130iterations 6.3967146E-03 0.1134987 at 140iterations 3.6185153E-03 6.1538696E-02 at 150iterations 2.0488705E-03 3.9665222E-02 at 160iterations 1.1645723E-03 2.0936489E-02 at 170iterations 6.6232937E-04 1.1871338E-02 at 180iterations finished qdiffx linear iterations at : 14:10:41 total time elapsed so far: 20.65000 # loops : 180 mean,max change (kT/e) : 6.6232937E-04 1.1871338E-02 energy calculations done at 20.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.82000 DelPhi exited at 14:10:41 20.827u 0.517s 0:21.80 97.8% 0+0k 0+0io 0pf+0w