Sun Oct 9 15:49:55 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 Sun Oct 9 2011 at 15:49:55 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 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: 0.5321535 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 0.5321535 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.4261 centred at (gu) : 90.53606 89.93710 89.05236 assigned negative charge : -826.3331 centred at (gu) : 90.47049 89.98900 88.94109 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9524 nv = 96 ne = 84 npr = 109666 no. pairs analyzed = 109666 no. exposed pairs = 6342 no. arc points = 44057 no. surface atoms = 2137 nbur = 3235 mkacc time = 0.1900000 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 = 1.596000 m= 381 mr = 5206 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3700000 number of dielectric boundary points 4682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4348 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1714120E-09 5.4738258E-10 midg,1,midg; midg,igrid,midg 2.8133634E-10 -4.6931120E-10 1,midg,midg; igrid,midg,midg -5.0390925E-10 4.3091691E-10 gauss-seidel spectral radius is 0.9819703 estimated iterations to convergence 61 setup time was (sec) 0.5600000 now iterating at: 15:49:56 rms-change max change #iterations 8.9587741E-02 11.29267 at 10iterations 8.4794024E-03 1.333023 at 20iterations 2.7992330E-03 0.4761086 at 30iterations 1.2046724E-03 0.2069130 at 40iterations 5.2222877E-04 9.0091705E-02 at 50iterations finished qdiffx linear iterations at : 15:49:59 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 5.2222877E-04 9.0091705E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:49:59 3.590u 0.156s 0:04.02 93.0% 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 Sun Oct 9 2011 at 15:49:59 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 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: 1.596460 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 1.596460 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.4261 centred at (gu) : 91.60600 89.80967 87.15519 assigned negative charge : -826.3331 centred at (gu) : 91.41140 89.96662 86.82327 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 107594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33610 mr = 76353 m= 3296 mr = 23164 m= 75 mr = 1459 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1826 time to turn everything in is 0.5200000 number of dielectric boundary points 43598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 532 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 39546 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) : 0.5321535 object centre at (A) : 71.56600 75.77200 1.219999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9254712E-02 1.8074117E-03 midg,1,midg; midg,igrid,midg -4.1890005E-03 -1.6550966E-02 1,midg,midg; igrid,midg,midg -1.2073349E-02 1.8637547E-02 gauss-seidel spectral radius is 0.9983187 estimated iterations to convergence 194 setup time was (sec) 0.7500000 now iterating at: 15:50:00 rms-change max change #iterations 4.546217 172.2645 at 10iterations 1.961234 56.18043 at 20iterations 0.8470095 24.59349 at 30iterations 0.3642344 9.925393 at 40iterations 0.1582694 4.603979 at 50iterations 6.8547763E-02 2.235992 at 60iterations 3.0334711E-02 0.8486786 at 70iterations 1.3745914E-02 0.4127579 at 80iterations 6.7629786E-03 0.2176552 at 90iterations 3.7643220E-03 0.1296844 at 100iterations 2.3847453E-03 9.1564178E-02 at 110iterations 1.6585389E-03 6.1614990E-02 at 120iterations finished qdiffx linear iterations at : 15:50:08 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.6585389E-03 6.1614990E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 15:50:08 8.087u 0.204s 0:08.55 96.8% 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 Sun Oct 9 2011 at 15:50:08 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5372 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 716 has a net charge of 1.4000 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: 2.394691 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): 38.61900 104.5130 ymin,ymax (A): 45.29400 106.2500 zmin,zma (A): -32.22900 34.66900 x,y,z range (A): 65.89400 60.95600 66.89799 scale (grids/A): 2.394691 object centre (A): 71.56600 75.77200 1.219999 number of atom coordinates read : 5372 total number of charged atoms : 5200 net assigned charge : -2.899957 assigned positive charge : 823.4261 centred at (gu) : 92.40846 89.71407 85.73229 assigned negative charge : -826.3331 centred at (gu) : 92.11703 89.94999 85.23486 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 250821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117042 mr = 186806 m= 32864 mr = 93291 m= 5059 mr = 24321 m= 282 mr = 3086 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 6065 time to turn everything in is 1.280000 number of dielectric boundary points 98475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 41540 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) : 1.596460 object centre at (A) : 71.56600 75.77200 1.219999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1342511 0.1263613 midg,1,midg; midg,igrid,midg -6.8057768E-02 -0.1718970 1,midg,midg; igrid,midg,midg -5.4128170E-02 0.3297364 gauss-seidel spectral radius is 0.9992264 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 15:50:10 rms-change max change #iterations 11.86195 395.5179 at 10iterations 6.905826 165.6215 at 20iterations 3.990627 83.11574 at 30iterations 2.301214 44.85830 at 40iterations 1.318297 23.67113 at 50iterations 0.7534355 13.46219 at 60iterations 0.4312714 7.124126 at 70iterations 0.2456840 4.094681 at 80iterations 0.1401504 2.256760 at 90iterations 7.9860404E-02 1.256012 at 100iterations 4.5536015E-02 0.8610497 at 110iterations 2.5903620E-02 0.4460936 at 120iterations 1.4807769E-02 0.2542152 at 130iterations 8.5184677E-03 0.1498208 at 140iterations 4.9538673E-03 9.9155426E-02 at 150iterations 2.9288069E-03 5.4599762E-02 at 160iterations 1.8020475E-03 3.4061432E-02 at 170iterations 1.1741122E-03 2.4322510E-02 at 180iterations finished qdiffx linear iterations at : 15:50:22 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.1741122E-03 2.4322510E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 15:50:22 13.506u 0.213s 0:13.99 97.9% 0+0k 0+0io 0pf+0w