Sun Oct 9 23:12:17 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 23:12:17 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: SEP 472 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5781285 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 0.5781285 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3606 net assigned charge : 2.025002 assigned positive charge : 567.1856 centred at (gu) : 90.28944 90.61190 89.84457 assigned negative charge : -565.1636 centred at (gu) : 90.18696 90.55080 89.65160 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8549 nv = 96 ne = 84 npr = 72985 no. pairs analyzed = 72985 no. exposed pairs = 4944 no. arc points = 34699 no. surface atoms = 1656 nbur = 2107 mkacc time = 0.1600000 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 = 1.484000 m= 406 mr = 4571 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3410 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9684314E-09 5.1778097E-09 midg,1,midg; midg,igrid,midg -1.0421981E-09 2.3206561E-09 1,midg,midg; igrid,midg,midg -2.1629691E-09 3.2935004E-09 gauss-seidel spectral radius is 0.9846309 estimated iterations to convergence 66 setup time was (sec) 0.6400000 now iterating at: 23:12:18 rms-change max change #iterations 0.1127584 16.27740 at 10iterations 8.7546399E-03 1.293920 at 20iterations 6.9361867E-04 9.3147278E-02 at 30iterations 5.7960766E-05 6.8168640E-03 at 40iterations 7.3380452E-06 1.2207031E-03 at 50iterations finished qdiffx linear iterations at : 23:12:21 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.3380452E-06 1.2207031E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 23:12:21 3.527u 0.199s 0:04.01 92.5% 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 23:12:21 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: SEP 472 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.734386 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 1.734386 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3606 net assigned charge : 2.025002 assigned positive charge : 567.1856 centred at (gu) : 90.86703 91.83433 89.53270 assigned negative charge : -565.1636 centred at (gu) : 90.56051 91.65182 88.95429 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 94310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34699 grid for indexing accessible points = 1.400000 m= 32622 mr = 65109 m= 4192 mr = 23245 m= 169 mr = 2366 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.6500000 number of dielectric boundary points 40515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 27974 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) : 0.5781285 object centre at (A) : -5.093501 -3.597001 -22.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3874162E-02 1.4267070E-02 midg,1,midg; midg,igrid,midg 1.9828886E-02 1.4727820E-02 1,midg,midg; igrid,midg,midg -1.8285913E-02 1.6503541E-03 gauss-seidel spectral radius is 0.9984893 estimated iterations to convergence 204 setup time was (sec) 0.9600000 now iterating at: 23:12:22 rms-change max change #iterations 4.350149 184.2992 at 10iterations 1.949252 71.54494 at 20iterations 0.8743967 25.78390 at 30iterations 0.3946449 14.00258 at 40iterations 0.1770969 5.929138 at 50iterations 7.9619773E-02 2.480400 at 60iterations 3.5740364E-02 1.118279 at 70iterations 1.6096579E-02 0.4966383 at 80iterations 7.2724172E-03 0.2169228 at 90iterations 3.2844620E-03 0.1038465 at 100iterations 1.4855376E-03 4.3242455E-02 at 110iterations 6.7213958E-04 1.8724442E-02 at 120iterations finished qdiffx linear iterations at : 23:12:30 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 6.7213958E-04 1.8724442E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 23:12:31 9.130u 0.239s 0:09.74 96.0% 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 23:12:31 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: SEP 472 has a net charge of -0.4750 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: 2.601578 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 2.601578 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3606 net assigned charge : 2.025002 assigned positive charge : 567.1856 centred at (gu) : 91.30033 92.75120 89.29878 assigned negative charge : -565.1636 centred at (gu) : 90.84061 92.47765 88.43121 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 218508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34699 grid for indexing accessible points = 1.400000 m= 109400 mr = 158624 m= 35257 mr = 87990 m= 7109 mr = 27358 m= 812 mr = 5106 m= 31 mr = 511 m= 0 mr = 6 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 961 time to turn everything in is 1.590000 number of dielectric boundary points 91522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 28833 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) : 1.734386 object centre at (A) : -5.093501 -3.597001 -22.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3762856 0.1472057 midg,1,midg; midg,igrid,midg 9.3517527E-02 0.3387420 1,midg,midg; igrid,midg,midg -0.2006962 -9.0490226E-03 gauss-seidel spectral radius is 0.9992552 estimated iterations to convergence 289 setup time was (sec) 1.920000 now iterating at: 23:12:33 rms-change max change #iterations 10.98904 293.2652 at 10iterations 6.545491 150.0331 at 20iterations 3.860391 84.19440 at 30iterations 2.267545 56.14105 at 40iterations 1.322471 29.04621 at 50iterations 0.7696567 16.85236 at 60iterations 0.4469578 8.687309 at 70iterations 0.2588638 4.953094 at 80iterations 0.1495229 2.943611 at 90iterations 8.6180255E-02 1.474783 at 100iterations 4.9789902E-02 1.034079 at 110iterations 2.8697424E-02 0.5191698 at 120iterations 1.6549936E-02 0.2876205 at 130iterations 9.5151244E-03 0.1586874 at 140iterations 5.4729874E-03 9.2144966E-02 at 150iterations 3.1561828E-03 5.4464340E-02 at 160iterations 1.8195849E-03 3.3065796E-02 at 170iterations 1.0534149E-03 1.7965794E-02 at 180iterations finished qdiffx linear iterations at : 23:12:44 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.0534149E-03 1.7965794E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 23:12:45 13.256u 0.246s 0:13.86 97.3% 0+0k 0+0io 0pf+0w