Sun Oct 9 06:46:07 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 Sun Oct 9 2011 at 06:46:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6625474 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): -24.94700 26.55600 ymin,ymax (A): 1.027000 46.26200 zmin,zma (A): -23.38500 30.34700 x,y,z range (A): 51.50300 45.23500 53.73200 scale (grids/A): 0.6625474 object centre (A): 0.8044996 23.64450 3.481000 number of atom coordinates read : 1998 total number of charged atoms : 1859 net assigned charge : -2.499985 assigned positive charge : 297.5140 centred at (gu) : 89.22267 89.59699 88.33318 assigned negative charge : -300.0141 centred at (gu) : 89.17198 89.81760 88.28921 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5867 nv = 96 ne = 84 npr = 42147 no. pairs analyzed = 42147 no. exposed pairs = 2490 no. arc points = 17563 no. surface atoms = 842 nbur = 1156 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3219 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2600000 number of dielectric boundary points 2920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1701 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6895 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9627414E-08 2.0775798E-10 midg,1,midg; midg,igrid,midg 3.0926444E-08 -3.9905807E-08 1,midg,midg; igrid,midg,midg -1.7599303E-08 1.2280376E-09 gauss-seidel spectral radius is 0.9881364 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 06:46:08 rms-change max change #iterations 0.1507047 26.09782 at 10iterations 1.6319558E-02 2.761468 at 20iterations 1.7379038E-03 0.2647858 at 30iterations 1.8439017E-04 3.0006409E-02 at 40iterations 1.9440662E-05 2.7008057E-03 at 50iterations finished qdiffx linear iterations at : 06:46:12 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 1.9440662E-05 2.7008057E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 06:46:12 4.517u 0.376s 0:05.16 94.5% 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 06:46:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 1.987642 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): -24.94700 26.55600 ymin,ymax (A): 1.027000 46.26200 zmin,zma (A): -23.38500 30.34700 x,y,z range (A): 51.50300 45.23500 53.73200 scale (grids/A): 1.987642 object centre (A): 0.8044996 23.64450 3.481000 number of atom coordinates read : 1998 total number of charged atoms : 1859 net assigned charge : -2.499985 assigned positive charge : 297.5140 centred at (gu) : 87.66788 88.79117 84.99962 assigned negative charge : -300.0141 centred at (gu) : 87.51613 89.45265 84.86767 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17563 grid for indexing accessible points = 1.400000 m= 22170 mr = 43668 m= 3456 mr = 16353 m= 211 mr = 2112 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 26958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14699 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) : 0.6625474 object centre at (A) : 0.8044996 23.64450 3.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9455542E-02 2.4100242E-02 midg,1,midg; midg,igrid,midg 4.7941234E-02 -3.1891327E-02 1,midg,midg; igrid,midg,midg -4.0952954E-02 -6.3636056E-03 gauss-seidel spectral radius is 0.9986789 estimated iterations to convergence 218 setup time was (sec) 0.8300000 now iterating at: 06:46:13 rms-change max change #iterations 4.030314 188.3161 at 10iterations 1.906981 78.92413 at 20iterations 0.9003104 32.39674 at 30iterations 0.4269894 15.26283 at 40iterations 0.2023673 6.821774 at 50iterations 9.5949598E-02 3.404880 at 60iterations 4.5405198E-02 1.553501 at 70iterations 2.1588022E-02 0.7186089 at 80iterations 1.0182493E-02 0.3758039 at 90iterations 4.8302561E-03 0.1565971 at 100iterations 2.2916184E-03 8.0824852E-02 at 110iterations 1.0913445E-03 4.0870667E-02 at 120iterations finished qdiffx linear iterations at : 06:46:23 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 1.0913445E-03 4.0870667E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 06:46:23 10.687u 0.442s 0:11.38 97.7% 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 06:46:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.981463 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): -24.94700 26.55600 ymin,ymax (A): 1.027000 46.26200 zmin,zma (A): -23.38500 30.34700 x,y,z range (A): 51.50300 45.23500 53.73200 scale (grids/A): 2.981463 object centre (A): 0.8044996 23.64450 3.481000 number of atom coordinates read : 1998 total number of charged atoms : 1859 net assigned charge : -2.499985 assigned positive charge : 297.5140 centred at (gu) : 86.50184 88.18671 82.49951 assigned negative charge : -300.0141 centred at (gu) : 86.27424 89.17902 82.30142 start vw surface at 0.1100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 146246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17563 grid for indexing accessible points = 1.400000 m= 72345 mr = 105750 m= 25572 mr = 59172 m= 6276 mr = 20448 m= 930 mr = 4660 m= 55 mr = 590 m= 0 mr = 26 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 60778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 14872 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) : 1.987642 object centre at (A) : 0.8044996 23.64450 3.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5572555 0.8047514 midg,1,midg; midg,igrid,midg 0.5748074 -0.3384383 1,midg,midg; igrid,midg,midg -0.3979713 4.7946882E-02 gauss-seidel spectral radius is 0.9992588 estimated iterations to convergence 290 setup time was (sec) 1.810000 now iterating at: 06:46:26 rms-change max change #iterations 9.228584 338.2111 at 10iterations 5.312646 132.8524 at 20iterations 3.063419 60.29050 at 30iterations 1.759241 38.62344 at 40iterations 1.011533 20.19191 at 50iterations 0.5812380 11.49025 at 60iterations 0.3336380 6.714406 at 70iterations 0.1916664 3.990169 at 80iterations 0.1096704 2.337405 at 90iterations 6.2941790E-02 1.265076 at 100iterations 3.6232743E-02 0.6496382 at 110iterations 2.0786183E-02 0.3816147 at 120iterations 1.1919807E-02 0.2221316 at 130iterations 6.8533826E-03 0.1297760 at 140iterations 3.9383881E-03 7.5651169E-02 at 150iterations 2.2613443E-03 4.8561096E-02 at 160iterations 1.3031421E-03 2.5412083E-02 at 170iterations 7.5589272E-04 1.5895426E-02 at 180iterations finished qdiffx linear iterations at : 06:46:42 total time elapsed so far: 17.82000 # loops : 180 mean,max change (kT/e) : 7.5589272E-04 1.5895426E-02 energy calculations done at 17.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 06:46:42 17.996u 0.466s 0:18.72 98.5% 0+0k 0+0io 0pf+0w