Sun Oct 9 09:04:56 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 09:04:56 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 381 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5807315 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 0.5807315 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4859979 assigned positive charge : 381.2315 centred at (gu) : 91.97636 90.39744 90.02219 assigned negative charge : -381.7185 centred at (gu) : 91.96076 90.25959 90.01637 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6323 nv = 96 ne = 84 npr = 57446 no. pairs analyzed = 57446 no. exposed pairs = 3568 no. arc points = 25516 no. surface atoms = 1212 nbur = 1569 mkacc time = 0.1200000 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 = 1.456000 m= 311 mr = 3165 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2474 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3616142E-10 -1.3159657E-11 midg,1,midg; midg,igrid,midg -2.5733509E-09 2.7384499E-09 1,midg,midg; igrid,midg,midg -2.6954630E-10 2.8623243E-10 gauss-seidel spectral radius is 0.9846916 estimated iterations to convergence 66 setup time was (sec) 0.6000000 now iterating at: 09:04:57 rms-change max change #iterations 9.2152953E-02 15.04311 at 10iterations 8.6661559E-03 1.409904 at 20iterations 2.4261202E-03 0.4665413 at 30iterations 1.1077176E-03 0.2188225 at 40iterations 5.2002550E-04 0.1025581 at 50iterations finished qdiffx linear iterations at : 09:05:00 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.2002550E-04 0.1025581 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:05:00 3.367u 0.205s 0:03.85 92.4% 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 Sun Oct 9 2011 at 09:05:00 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 381 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.742194 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 1.742194 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4859979 assigned positive charge : 381.2315 centred at (gu) : 95.92844 91.19183 90.06607 assigned negative charge : -381.7185 centred at (gu) : 95.88184 90.77849 90.04890 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25516 grid for indexing accessible points = 1.400000 m= 23400 mr = 45498 m= 3499 mr = 16355 m= 133 mr = 2112 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 31904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20616 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) : 0.5807315 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3811321E-03 -5.5620703E-03 midg,1,midg; midg,igrid,midg -6.7048268E-03 1.1537855E-02 1,midg,midg; igrid,midg,midg 8.0296188E-04 5.9112650E-04 gauss-seidel spectral radius is 0.9984004 estimated iterations to convergence 198 setup time was (sec) 0.8300000 now iterating at: 09:05:01 rms-change max change #iterations 3.498267 142.6704 at 10iterations 1.528264 59.87731 at 20iterations 0.6713923 24.57032 at 30iterations 0.2964523 10.35073 at 40iterations 0.1306416 4.395679 at 50iterations 5.7752058E-02 1.956732 at 60iterations 2.6135208E-02 0.8481817 at 70iterations 1.2373563E-02 0.4742393 at 80iterations 6.4926217E-03 0.2518501 at 90iterations 3.9659571E-03 0.1702995 at 100iterations 2.7381720E-03 0.1074677 at 110iterations 2.0278352E-03 7.9471588E-02 at 120iterations finished qdiffx linear iterations at : 09:05:08 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 2.0278352E-03 7.9471588E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 09:05:08 7.539u 0.241s 0:08.05 96.5% 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 09:05:08 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 381 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.613292 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 2.613292 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4859979 assigned positive charge : 381.2315 centred at (gu) : 98.89249 91.78757 90.09884 assigned negative charge : -381.7185 centred at (gu) : 98.82281 91.16767 90.07329 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 159619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25516 grid for indexing accessible points = 1.400000 m= 75959 mr = 111687 m= 27314 mr = 59771 m= 6107 mr = 21257 m= 614 mr = 4471 m= 12 mr = 378 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 72061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21200 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) : 1.742194 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1318794 -9.0696596E-02 midg,1,midg; midg,igrid,midg -9.1432696E-03 9.4998799E-02 1,midg,midg; igrid,midg,midg 7.0317243E-03 -6.7013791E-03 gauss-seidel spectral radius is 0.9992032 estimated iterations to convergence 280 setup time was (sec) 1.530000 now iterating at: 09:05:10 rms-change max change #iterations 8.742600 277.7349 at 10iterations 5.038258 126.1809 at 20iterations 2.902335 65.56253 at 30iterations 1.655579 35.62055 at 40iterations 0.9431598 19.81026 at 50iterations 0.5354444 11.02964 at 60iterations 0.3033347 6.028961 at 70iterations 0.1717689 3.312721 at 80iterations 9.7076915E-02 2.193813 at 90iterations 5.4953445E-02 1.017945 at 100iterations 3.1124119E-02 0.6793613 at 110iterations 1.7697079E-02 0.3677979 at 120iterations 1.0183597E-02 0.2213631 at 130iterations 5.9981383E-03 0.1441765 at 140iterations 3.6928500E-03 8.7253571E-02 at 150iterations 2.4359205E-03 6.0146332E-02 at 160iterations 1.7504439E-03 4.0870667E-02 at 170iterations 1.3540213E-03 3.0429840E-02 at 180iterations finished qdiffx linear iterations at : 09:05:21 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 1.3540213E-03 3.0429840E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 09:05:21 12.184u 0.257s 0:12.77 97.3% 0+0k 0+0io 0pf+0w