Tue Oct 11 01:15:26 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 Tue Oct 11 2011 at 01:15:26 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 = 2714 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.5636836 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): 6.881999 70.03800 ymin,ymax (A): -11.27900 43.70500 zmin,zma (A): -17.95000 25.12400 x,y,z range (A): 63.15600 54.98400 43.07400 scale (grids/A): 0.5636836 object centre (A): 38.46000 16.21300 3.587001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 6.500020 assigned positive charge : 410.5715 centred at (gu) : 92.44855 89.72469 90.04958 assigned negative charge : -404.0723 centred at (gu) : 92.26505 89.87837 89.90536 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5549 nv = 96 ne = 84 npr = 54685 no. pairs analyzed = 54685 no. exposed pairs = 3248 no. arc points = 22708 no. surface atoms = 1103 nbur = 1611 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 = 1.540000 m= 226 mr = 3026 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2290 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3400743E-10 2.3714439E-09 midg,1,midg; midg,igrid,midg 2.6154661E-09 -9.8663056E-10 1,midg,midg; igrid,midg,midg -7.6946172E-10 5.0511946E-09 gauss-seidel spectral radius is 0.9837366 estimated iterations to convergence 64 setup time was (sec) 0.8700000 now iterating at: 01:15:27 rms-change max change #iterations 8.1438772E-02 13.00641 at 10iterations 6.8791290E-03 1.366276 at 20iterations 9.7947789E-04 0.2545815 at 30iterations 2.4245487E-04 6.7359924E-02 at 40iterations 6.4716442E-05 1.8169403E-02 at 50iterations finished qdiffx linear iterations at : 01:15:35 total time elapsed so far: 8.490000 # loops : 50 mean,max change (kT/e) : 6.4716442E-05 1.8169403E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 01:15:36 8.716u 0.680s 0:10.10 92.9% 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 Tue Oct 11 2011 at 01:15:36 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 = 2714 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.691051 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): 6.881999 70.03800 ymin,ymax (A): -11.27900 43.70500 zmin,zma (A): -17.95000 25.12400 x,y,z range (A): 63.15600 54.98400 43.07400 scale (grids/A): 1.691051 object centre (A): 38.46000 16.21300 3.587001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 6.500020 assigned positive charge : 410.5715 centred at (gu) : 97.34521 89.17336 90.14790 assigned negative charge : -404.0723 centred at (gu) : 96.79478 89.63504 89.71590 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 61703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22708 grid for indexing accessible points = 1.400000 m= 19207 mr = 42871 m= 2211 mr = 13774 m= 61 mr = 1254 m= 0 mr = 8 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 137 time to turn everything in is 0.7000000 number of dielectric boundary points 25275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19863 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) : 0.5636836 object centre at (A) : 38.46000 16.21300 3.587001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6887321E-03 1.5170890E-02 midg,1,midg; midg,igrid,midg 1.7878307E-02 -1.3412301E-02 1,midg,midg; igrid,midg,midg 1.0052572E-02 4.3863850E-03 gauss-seidel spectral radius is 0.9982737 estimated iterations to convergence 191 setup time was (sec) 1.220000 now iterating at: 01:15:38 rms-change max change #iterations 3.381992 147.2243 at 10iterations 1.432285 55.95920 at 20iterations 0.6109360 21.82480 at 30iterations 0.2614478 9.379181 at 40iterations 0.1115534 4.109960 at 50iterations 4.7667406E-02 1.923100 at 60iterations 2.0380719E-02 0.7593803 at 70iterations 8.8490043E-03 0.3120995 at 80iterations 3.8793955E-03 0.1655731 at 90iterations 1.7612596E-03 7.7709198E-02 at 100iterations 8.4335177E-04 3.7334442E-02 at 110iterations 4.2558540E-04 2.1755219E-02 at 120iterations finished qdiffx linear iterations at : 01:15:55 total time elapsed so far: 18.60000 # loops : 120 mean,max change (kT/e) : 4.2558540E-04 2.1755219E-02 energy calculations done at 18.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.83000 DelPhi exited at 01:15:56 18.832u 0.764s 0:20.13 97.3% 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 Tue Oct 11 2011 at 01:15:56 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 = 2714 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.536576 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): 6.881999 70.03800 ymin,ymax (A): -11.27900 43.70500 zmin,zma (A): -17.95000 25.12400 x,y,z range (A): 63.15600 54.98400 43.07400 scale (grids/A): 2.536576 object centre (A): 38.46000 16.21300 3.587001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 6.500020 assigned positive charge : 410.5715 centred at (gu) : 101.0179 88.75983 90.22183 assigned negative charge : -404.0723 centred at (gu) : 100.1921 89.45237 89.57377 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 143763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22708 grid for indexing accessible points = 1.400000 m= 66585 mr = 104898 m= 19751 mr = 53851 m= 3555 mr = 15436 m= 268 mr = 2610 m= 3 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 507 time to turn everything in is 1.720000 number of dielectric boundary points 57003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 20552 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) : 1.691051 object centre at (A) : 38.46000 16.21300 3.587001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9578118E-02 0.1865531 midg,1,midg; midg,igrid,midg 0.2238757 -0.2687432 1,midg,midg; igrid,midg,midg 0.3028741 -6.5413743E-02 gauss-seidel spectral radius is 0.9991534 estimated iterations to convergence 271 setup time was (sec) 2.310000 now iterating at: 01:15:59 rms-change max change #iterations 8.411395 249.6488 at 10iterations 4.663390 114.8540 at 20iterations 2.588434 53.47235 at 30iterations 1.437920 30.59208 at 40iterations 0.7946259 16.53203 at 50iterations 0.4391469 8.825310 at 60iterations 0.2426604 5.044403 at 70iterations 0.1340145 2.836628 at 80iterations 7.3984526E-02 1.562828 at 90iterations 4.0846996E-02 0.8841438 at 100iterations 2.2607585E-02 0.4625816 at 110iterations 1.2561406E-02 0.2728376 at 120iterations 7.0137889E-03 0.1380424 at 130iterations 3.9390349E-03 8.4539413E-02 at 140iterations 2.2593867E-03 5.5477142E-02 at 150iterations 1.3289303E-03 3.2295227E-02 at 160iterations 8.1119774E-04 2.3063660E-02 at 170iterations 5.1731436E-04 1.5522003E-02 at 180iterations finished qdiffx linear iterations at : 01:16:28 total time elapsed so far: 30.87000 # loops : 180 mean,max change (kT/e) : 5.1731436E-04 1.5522003E-02 energy calculations done at 30.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.10000 DelPhi exited at 01:16:28 31.106u 0.788s 0:32.21 98.9% 0+0k 0+0io 0pf+0w