Sat Oct 8 13:31:24 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 Sat Oct 8 2011 at 13:31:24 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6384848 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 0.6384848 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9859930 assigned positive charge : 452.0976 centred at (gu) : 88.80441 89.63668 92.24589 assigned negative charge : -453.0843 centred at (gu) : 88.74340 89.54348 92.15166 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8279 nv = 96 ne = 84 npr = 62968 no. pairs analyzed = 62968 no. exposed pairs = 3461 no. arc points = 23696 no. surface atoms = 1182 nbur = 1836 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4921 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2260 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5537231E-09 1.7494409E-08 midg,1,midg; midg,igrid,midg -1.4849403E-08 9.6634345E-09 1,midg,midg; igrid,midg,midg -1.2301556E-08 4.8918021E-09 gauss-seidel spectral radius is 0.9873224 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 13:31:25 rms-change max change #iterations 0.1594373 23.80210 at 10iterations 1.6037550E-02 2.036949 at 20iterations 1.7498536E-03 0.2727509 at 30iterations 2.6884294E-04 3.8434982E-02 at 40iterations 5.7284964E-05 9.5405579E-03 at 50iterations finished qdiffx linear iterations at : 13:31:29 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 5.7284964E-05 9.5405579E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 13:31:29 4.233u 0.238s 0:04.77 93.5% 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 Sat Oct 8 2011 at 13:31:29 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.915455 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 1.915455 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9859930 assigned positive charge : 452.0976 centred at (gu) : 86.41264 88.90936 96.73711 assigned negative charge : -453.0843 centred at (gu) : 86.22971 88.63008 96.45458 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 34027 mr = 65460 m= 5498 mr = 26066 m= 307 mr = 3467 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22619 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) : 0.6384848 object centre at (A) : 15.77450 -3.3499718E-02 19.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3173681E-02 2.4911225E-02 midg,1,midg; midg,igrid,midg -2.8424163E-03 1.5483367E-02 1,midg,midg; igrid,midg,midg -6.5495849E-02 1.3515577E-02 gauss-seidel spectral radius is 0.9986821 estimated iterations to convergence 218 setup time was (sec) 1.000000 now iterating at: 13:31:31 rms-change max change #iterations 4.708776 198.2048 at 10iterations 2.247871 63.88549 at 20iterations 1.066850 32.39327 at 30iterations 0.5075945 14.36307 at 40iterations 0.2404359 6.836640 at 50iterations 0.1149630 3.301482 at 60iterations 5.4779235E-02 1.652101 at 70iterations 2.5911381E-02 0.7521982 at 80iterations 1.2425425E-02 0.3740940 at 90iterations 5.9281914E-03 0.1817093 at 100iterations 2.8418601E-03 9.4238281E-02 at 110iterations 1.3683215E-03 3.6840439E-02 at 120iterations finished qdiffx linear iterations at : 13:31:39 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 1.3683215E-03 3.6840439E-02 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 13:31:40 9.782u 0.253s 0:10.33 97.0% 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 Sat Oct 8 2011 at 13:31:40 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.873182 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 2.873182 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9859930 assigned positive charge : 452.0976 centred at (gu) : 84.61893 88.36393 100.1055 assigned negative charge : -453.0843 centred at (gu) : 84.34464 87.94511 99.68196 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 207955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 109728 mr = 157666 m= 40928 mr = 92012 m= 9835 mr = 33526 m= 1399 mr = 7560 m= 58 mr = 880 m= 0 mr = 16 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 78243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 22968 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) : 1.915455 object centre at (A) : 15.77450 -3.3499718E-02 19.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1050212 0.3074319 midg,1,midg; midg,igrid,midg 1.4832117E-02 0.1874850 1,midg,midg; igrid,midg,midg -0.9229141 0.2299291 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.160000 now iterating at: 13:31:42 rms-change max change #iterations 10.98878 422.2584 at 10iterations 6.476385 171.4482 at 20iterations 3.794768 80.50713 at 30iterations 2.220306 44.68699 at 40iterations 1.290090 23.54188 at 50iterations 0.7520875 13.58370 at 60iterations 0.4368564 7.745281 at 70iterations 0.2537476 4.523530 at 80iterations 0.1472689 2.405289 at 90iterations 8.5351586E-02 1.570871 at 100iterations 4.9561564E-02 0.8004322 at 110iterations 2.8694706E-02 0.4700508 at 120iterations 1.6635962E-02 0.2618599 at 130iterations 9.6647926E-03 0.1597323 at 140iterations 5.6033656E-03 9.7926617E-02 at 150iterations 3.2611692E-03 5.1767349E-02 at 160iterations 1.9076855E-03 3.2556534E-02 at 170iterations 1.1242231E-03 1.8030167E-02 at 180iterations finished qdiffx linear iterations at : 13:31:57 total time elapsed so far: 16.77000 # loops : 180 mean,max change (kT/e) : 1.1242231E-03 1.8030167E-02 energy calculations done at 16.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.95000 DelPhi exited at 13:31:57 16.949u 0.354s 0:17.60 98.2% 0+0k 0+0io 0pf+0w