Sat Oct 15 14:35:01 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 15 2011 at 14:35:06 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6216168 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 0.6216168 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.485981 assigned positive charge : 431.7931 centred at (gu) : 89.23877 89.60271 88.83147 assigned negative charge : -435.2802 centred at (gu) : 89.16998 89.54314 88.84338 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7414 nv = 96 ne = 84 npr = 57664 no. pairs analyzed = 57664 no. exposed pairs = 3671 no. arc points = 26422 no. surface atoms = 1238 nbur = 1616 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3935 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2200000 number of dielectric boundary points 3815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9088 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4958402E-09 -2.9728491E-09 midg,1,midg; midg,igrid,midg -8.2512761E-09 1.5685618E-09 1,midg,midg; igrid,midg,midg -9.8089439E-09 2.0344406E-09 gauss-seidel spectral radius is 0.9866254 estimated iterations to convergence 71 setup time was (sec) 0.4400000 now iterating at: 14:35:09 rms-change max change #iterations 0.1355777 19.09355 at 10iterations 1.2677472E-02 1.733635 at 20iterations 1.1697018E-03 0.1784363 at 30iterations 1.0931931E-04 1.5404224E-02 at 40iterations 1.0161416E-05 1.2712479E-03 at 50iterations finished qdiffx linear iterations at : 14:35:19 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.0161416E-05 1.2712479E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 14:35:20 3.977u 0.224s 0:15.01 27.9% 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 15 2011 at 14:35:21 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.864851 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 1.864851 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.485981 assigned positive charge : 431.7931 centred at (gu) : 87.71568 88.80762 86.49339 assigned negative charge : -435.2802 centred at (gu) : 87.50974 88.62918 86.52944 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 26918 mr = 54594 m= 3767 mr = 19126 m= 184 mr = 2164 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 0.4300000 number of dielectric boundary points 35309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 21315 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) : 0.6216168 object centre at (A) : 19.85400 15.45500 27.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2507387E-02 -1.5549411E-02 midg,1,midg; midg,igrid,midg -2.0942831E-02 -9.8518596E-04 1,midg,midg; igrid,midg,midg -5.4265305E-02 2.4024028E-02 gauss-seidel spectral radius is 0.9986068 estimated iterations to convergence 212 setup time was (sec) 0.7200000 now iterating at: 14:35:23 rms-change max change #iterations 4.332390 185.0137 at 10iterations 2.010538 66.29008 at 20iterations 0.9328915 30.15644 at 30iterations 0.4317510 13.65740 at 40iterations 0.2010217 6.913208 at 50iterations 9.3282625E-02 3.210620 at 60iterations 4.3310829E-02 1.375321 at 70iterations 2.0094419E-02 0.6053009 at 80iterations 9.3446029E-03 0.3070202 at 90iterations 4.3377616E-03 0.1413994 at 100iterations 2.0199998E-03 6.5906048E-02 at 110iterations 9.3703531E-04 2.8735161E-02 at 120iterations finished qdiffx linear iterations at : 14:35:45 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 9.3703531E-04 2.8735161E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 14:35:46 9.684u 0.307s 0:24.70 40.4% 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 15 2011 at 14:35:47 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.797276 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 2.797276 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.485981 assigned positive charge : 431.7931 centred at (gu) : 86.57323 88.21117 84.73987 assigned negative charge : -435.2802 centred at (gu) : 86.26460 87.94365 84.79419 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 186159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 89261 mr = 132963 m= 29894 mr = 71541 m= 6387 mr = 23263 m= 795 mr = 4635 m= 27 mr = 458 m= 0 mr = 13 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 2719 time to turn everything in is 1.090000 number of dielectric boundary points 79650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21703 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) : 1.864851 object centre at (A) : 19.85400 15.45500 27.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2544461 -0.4547334 midg,1,midg; midg,igrid,midg -0.2072043 -2.1809960E-02 1,midg,midg; igrid,midg,midg -0.6599199 0.3372964 gauss-seidel spectral radius is 0.9992709 estimated iterations to convergence 292 setup time was (sec) 1.400000 now iterating at: 14:35:50 rms-change max change #iterations 10.55277 349.9296 at 10iterations 6.269617 150.0475 at 20iterations 3.686303 87.47007 at 30iterations 2.159805 48.39843 at 40iterations 1.257768 24.50029 at 50iterations 0.7332323 15.84678 at 60iterations 0.4255920 7.761383 at 70iterations 0.2470900 4.940911 at 80iterations 0.1433485 2.865208 at 90iterations 8.2847640E-02 1.812560 at 100iterations 4.7893930E-02 0.8398285 at 110iterations 2.7694078E-02 0.5393238 at 120iterations 1.6007774E-02 0.2846384 at 130iterations 9.2601785E-03 0.1830835 at 140iterations 5.3455289E-03 9.4619751E-02 at 150iterations 3.0873783E-03 6.0248375E-02 at 160iterations 1.7820357E-03 3.1345367E-02 at 170iterations 1.0298807E-03 1.7046981E-02 at 180iterations finished qdiffx linear iterations at : 14:36:20 total time elapsed so far: 15.90000 # loops : 180 mean,max change (kT/e) : 1.0298807E-03 1.7046981E-02 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 14:36:21 16.032u 0.338s 0:33.81 48.3% 0+0k 0+0io 0pf+0w