Sat Oct 8 13:08:35 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 13:08:35 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5740639 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): -5.614000 43.29700 ymin,ymax (A): -23.57900 28.15700 zmin,zma (A): -8.743999 53.27000 x,y,z range (A): 48.91100 51.73600 62.01400 scale (grids/A): 0.5740639 object centre (A): 18.84150 2.289000 22.26300 number of atom coordinates read : 3122 total number of charged atoms : 2974 net assigned charge : 3.226028 assigned positive charge : 468.1238 centred at (gu) : 89.03810 89.88285 90.27848 assigned negative charge : -464.8988 centred at (gu) : 88.97683 89.92149 90.44326 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6719 nv = 96 ne = 84 npr = 63970 no. pairs analyzed = 63970 no. exposed pairs = 3793 no. arc points = 26610 no. surface atoms = 1283 nbur = 1839 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 = 1.512000 m= 296 mr = 3710 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3900000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2768 ## 341 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4095213E-09 -2.7548341E-09 midg,1,midg; midg,igrid,midg 1.3588720E-09 -1.3124445E-10 1,midg,midg; igrid,midg,midg -7.2502288E-10 1.3902468E-09 gauss-seidel spectral radius is 0.9843493 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 13:08:36 rms-change max change #iterations 9.7286329E-02 15.23695 at 10iterations 8.0182524E-03 1.305370 at 20iterations 1.4386822E-03 0.3005066 at 30iterations 5.8706262E-04 0.1295033 at 40iterations 2.5632279E-04 5.6766510E-02 at 50iterations finished qdiffx linear iterations at : 13:08:40 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 2.5632279E-04 5.6766510E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 13:08:40 4.265u 0.288s 0:04.82 94.1% 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 13:08:40 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.722192 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): -5.614000 43.29700 ymin,ymax (A): -23.57900 28.15700 zmin,zma (A): -8.743999 53.27000 x,y,z range (A): 48.91100 51.73600 62.01400 scale (grids/A): 1.722192 object centre (A): 18.84150 2.289000 22.26300 number of atom coordinates read : 3122 total number of charged atoms : 2974 net assigned charge : 3.226028 assigned positive charge : 468.1238 centred at (gu) : 87.11352 89.64760 90.83426 assigned negative charge : -464.8988 centred at (gu) : 86.93012 89.76393 91.32927 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26610 grid for indexing accessible points = 1.400000 m= 24634 mr = 52081 m= 3079 mr = 17654 m= 110 mr = 1755 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 828 time to turn everything in is 0.6500000 number of dielectric boundary points 30623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23011 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) : 0.5740639 object centre at (A) : 18.84150 2.289000 22.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1919964E-02 1.4905787E-02 midg,1,midg; midg,igrid,midg 2.9927616E-03 3.0199841E-03 1,midg,midg; igrid,midg,midg -1.5952999E-03 1.8222688E-03 gauss-seidel spectral radius is 0.9983878 estimated iterations to convergence 198 setup time was (sec) 0.9600000 now iterating at: 13:08:41 rms-change max change #iterations 3.840951 183.0733 at 10iterations 1.677807 71.13316 at 20iterations 0.7343395 23.42005 at 30iterations 0.3222797 11.05543 at 40iterations 0.1413315 4.532843 at 50iterations 6.2273074E-02 2.051064 at 60iterations 2.7511217E-02 0.8764682 at 70iterations 1.2248431E-02 0.3920288 at 80iterations 5.6325807E-03 0.2143555 at 90iterations 2.7676811E-03 0.1116657 at 100iterations 1.5332989E-03 6.3759804E-02 at 110iterations 9.7520679E-04 4.2976379E-02 at 120iterations finished qdiffx linear iterations at : 13:08:50 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 9.7520679E-04 4.2976379E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 13:08:51 9.760u 0.326s 0:10.40 96.9% 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 Sat Oct 8 2011 at 13:08:51 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.583288 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): -5.614000 43.29700 ymin,ymax (A): -23.57900 28.15700 zmin,zma (A): -8.743999 53.27000 x,y,z range (A): 48.91100 51.73600 62.01400 scale (grids/A): 2.583288 object centre (A): 18.84150 2.289000 22.26300 number of atom coordinates read : 3122 total number of charged atoms : 2974 net assigned charge : 3.226028 assigned positive charge : 468.1238 centred at (gu) : 85.67012 89.47130 91.25134 assigned negative charge : -464.8988 centred at (gu) : 85.39516 89.64565 91.99369 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 172523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26610 grid for indexing accessible points = 1.400000 m= 82969 mr = 126527 m= 26286 mr = 67305 m= 5208 mr = 20599 m= 488 mr = 3758 m= 14 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2765 time to turn everything in is 1.620000 number of dielectric boundary points 69048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 23772 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) : 1.722192 object centre at (A) : 18.84150 2.289000 22.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7205556E-02 0.3507989 midg,1,midg; midg,igrid,midg 3.9583270E-02 7.4828759E-02 1,midg,midg; igrid,midg,midg -2.1200104E-02 -2.2111360E-02 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.970000 now iterating at: 13:08:53 rms-change max change #iterations 9.577819 273.0262 at 10iterations 5.479482 154.8563 at 20iterations 3.118191 63.60363 at 30iterations 1.774775 35.64763 at 40iterations 1.002775 19.42350 at 50iterations 0.5660467 12.23981 at 60iterations 0.3205220 7.094236 at 70iterations 0.1805938 3.564590 at 80iterations 0.1018665 2.346943 at 90iterations 5.7406954E-02 1.075890 at 100iterations 3.2379679E-02 0.6280670 at 110iterations 1.8236684E-02 0.3639202 at 120iterations 1.0310186E-02 0.2019253 at 130iterations 5.8639874E-03 0.1262817 at 140iterations 3.3744229E-03 7.5622559E-02 at 150iterations 1.9878533E-03 4.8557281E-02 at 160iterations 1.2249341E-03 3.2840729E-02 at 170iterations 8.0517377E-04 2.0309448E-02 at 180iterations finished qdiffx linear iterations at : 13:09:07 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 8.0517377E-04 2.0309448E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 13:09:08 16.637u 0.358s 0:17.28 98.2% 0+0k 0+0io 0pf+0w