Wed Dec 21 14:21:58 PST 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 Wed Dec 21 2011 at 14:22:00 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1931 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 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: 0.6149594 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): -8.920000 48.97000 ymin,ymax (A): 8.456000 47.65300 zmin,zma (A): -3.597000 38.98000 x,y,z range (A): 57.89000 39.19700 42.57700 scale (grids/A): 0.6149594 object centre (A): 20.02500 28.05450 17.69150 number of atom coordinates read : 1931 total number of charged atoms : 1799 net assigned charge : -0.8999896 assigned positive charge : 286.3420 centred at (gu) : 90.11312 89.70715 90.45883 assigned negative charge : -287.2423 centred at (gu) : 90.10167 89.66995 90.58902 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4919 nv = 96 ne = 84 npr = 39878 no. pairs analyzed = 39878 no. exposed pairs = 2425 no. arc points = 16909 no. surface atoms = 820 nbur = 1111 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 209 mr = 2738 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5923 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3831769E-09 -6.8699277E-09 midg,1,midg; midg,igrid,midg -2.3157563E-09 9.2415864E-10 1,midg,midg; igrid,midg,midg -1.0439056E-09 -9.9240942E-11 gauss-seidel spectral radius is 0.9862502 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 14:22:01 rms-change max change #iterations 0.1078311 20.05444 at 10iterations 9.7865118E-03 1.676758 at 20iterations 8.7403168E-04 0.1699972 at 30iterations 7.7448247E-05 1.2262344E-02 at 40iterations 7.1415902E-06 1.5106201E-03 at 50iterations finished qdiffx linear iterations at : 14:22:05 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 7.1415902E-06 1.5106201E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 14:22:10 4.585u 0.372s 0:10.62 46.6% 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 Wed Dec 21 2011 at 14:22:12 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1931 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 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: 1.844878 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): -8.920000 48.97000 ymin,ymax (A): 8.456000 47.65300 zmin,zma (A): -3.597000 38.98000 x,y,z range (A): 57.89000 39.19700 42.57700 scale (grids/A): 1.844878 object centre (A): 20.02500 28.05450 17.69150 number of atom coordinates read : 1931 total number of charged atoms : 1799 net assigned charge : -0.8999896 assigned positive charge : 286.3420 centred at (gu) : 90.33950 89.12151 91.37659 assigned negative charge : -287.2423 centred at (gu) : 90.30516 89.01002 91.76743 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 53579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16909 grid for indexing accessible points = 1.400000 m= 18013 mr = 37004 m= 2319 mr = 13426 m= 90 mr = 1455 m= 0 mr = 28 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1777 time to turn everything in is 0.4300000 number of dielectric boundary points 22088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14145 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) : 0.6149594 object centre at (A) : 20.02500 28.05450 17.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9383807E-03 -1.3600837E-02 midg,1,midg; midg,igrid,midg 1.0567042E-04 1.7198862E-03 1,midg,midg; igrid,midg,midg 1.7494641E-02 2.7012503E-02 gauss-seidel spectral radius is 0.9984660 estimated iterations to convergence 203 setup time was (sec) 0.7600000 now iterating at: 14:22:14 rms-change max change #iterations 3.385087 162.8383 at 10iterations 1.507688 60.68563 at 20iterations 0.6761028 27.21164 at 30iterations 0.3024291 13.59604 at 40iterations 0.1355017 4.883072 at 50iterations 6.0507424E-02 2.805584 at 60iterations 2.7017232E-02 1.039524 at 70iterations 1.2104850E-02 0.4672260 at 80iterations 5.4375823E-03 0.2248974 at 90iterations 2.4315231E-03 8.9357376E-02 at 100iterations 1.0876360E-03 4.1874766E-02 at 110iterations 4.8732237E-04 1.7221451E-02 at 120iterations finished qdiffx linear iterations at : 14:22:24 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 4.8732237E-04 1.7221451E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:22:27 10.850u 0.445s 0:14.52 77.7% 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 Wed Dec 21 2011 at 14:22:28 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1931 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 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: 2.767317 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): -8.920000 48.97000 ymin,ymax (A): 8.456000 47.65300 zmin,zma (A): -3.597000 38.98000 x,y,z range (A): 57.89000 39.19700 42.57700 scale (grids/A): 2.767317 object centre (A): 20.02500 28.05450 17.69150 number of atom coordinates read : 1931 total number of charged atoms : 1799 net assigned charge : -0.8999896 assigned positive charge : 286.3420 centred at (gu) : 90.50924 88.68219 92.06477 assigned negative charge : -287.2423 centred at (gu) : 90.45773 88.51514 92.65119 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 124250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16909 grid for indexing accessible points = 1.400000 m= 60624 mr = 89943 m= 19631 mr = 49974 m= 3922 mr = 15843 m= 372 mr = 2948 m= 13 mr = 248 m= 0 mr = 6 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 5997 time to turn everything in is 1.090000 number of dielectric boundary points 49850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 14391 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) : 1.844878 object centre at (A) : 20.02500 28.05450 17.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5022251E-02 -0.1349550 midg,1,midg; midg,igrid,midg 3.9953396E-02 2.5033820E-02 1,midg,midg; igrid,midg,midg 0.2595346 0.3853764 gauss-seidel spectral radius is 0.9991946 estimated iterations to convergence 278 setup time was (sec) 1.410000 now iterating at: 14:22:30 rms-change max change #iterations 8.069912 357.0102 at 10iterations 4.571904 118.6676 at 20iterations 2.577121 65.59706 at 30iterations 1.447679 30.47638 at 40iterations 0.8136546 19.92467 at 50iterations 0.4559025 9.947140 at 60iterations 0.2554205 5.512486 at 70iterations 0.1433909 3.316574 at 80iterations 7.9998389E-02 1.833931 at 90iterations 4.4918854E-02 0.8838952 at 100iterations 2.5143061E-02 0.5661850 at 110iterations 1.4070494E-02 0.2883139 at 120iterations 7.8887101E-03 0.1600113 at 130iterations 4.4185049E-03 0.1091080 at 140iterations 2.4719778E-03 5.4838181E-02 at 150iterations 1.3811192E-03 2.8645515E-02 at 160iterations 7.7450887E-04 1.6480565E-02 at 170iterations 4.3321861E-04 9.0751648E-03 at 180iterations finished qdiffx linear iterations at : 14:22:46 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 4.3321861E-04 9.0751648E-03 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.42000 DelPhi exited at 14:22:50 17.421u 0.451s 0:22.54 79.2% 0+0k 0+0io 0pf+0w