Sat Oct 8 15:02:56 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 Sat Oct 8 2011 at 15:02:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6041783 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 0.6041783 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3118 net assigned charge : 3.025009 assigned positive charge : 491.5638 centred at (gu) : 92.02113 89.25419 90.07061 assigned negative charge : -488.5401 centred at (gu) : 92.06229 89.28560 90.09757 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7850 nv = 96 ne = 84 npr = 67549 no. pairs analyzed = 67549 no. exposed pairs = 3718 no. arc points = 26120 no. surface atoms = 1268 nbur = 1998 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 = 1.456000 m= 373 mr = 4507 m= 0 mr = 29 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3800000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2682 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8633713E-09 1.0750376E-10 midg,1,midg; midg,igrid,midg 3.7128802E-09 -9.4916318E-11 1,midg,midg; igrid,midg,midg 2.3234472E-09 -1.0762615E-09 gauss-seidel spectral radius is 0.9858699 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 15:02:57 rms-change max change #iterations 0.1284467 15.99000 at 10iterations 1.1404044E-02 1.499321 at 20iterations 1.0702753E-03 0.1455903 at 30iterations 1.2531139E-04 1.8093109E-02 at 40iterations 2.5044927E-05 4.0616989E-03 at 50iterations finished qdiffx linear iterations at : 15:03:00 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.5044927E-05 4.0616989E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 15:03:01 4.576u 0.382s 0:05.27 93.9% 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 15:03:01 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.812535 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 1.812535 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3118 net assigned charge : 3.025009 assigned positive charge : 491.5638 centred at (gu) : 96.06236 87.76154 90.21069 assigned negative charge : -488.5401 centred at (gu) : 96.18660 87.85639 90.29241 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26120 grid for indexing accessible points = 1.400000 m= 30015 mr = 61716 m= 4065 mr = 22211 m= 168 mr = 2435 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1880 time to turn everything in is 0.6800000 number of dielectric boundary points 33899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 24409 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) : 0.6041783 object centre at (A) : 27.85450 1.431500 18.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7930560E-03 -2.0293687E-02 midg,1,midg; midg,igrid,midg 7.2556515E-03 6.5989932E-03 1,midg,midg; igrid,midg,midg 3.1671159E-02 1.2267064E-02 gauss-seidel spectral radius is 0.9985538 estimated iterations to convergence 208 setup time was (sec) 0.9700000 now iterating at: 15:03:02 rms-change max change #iterations 4.381227 176.8848 at 10iterations 1.991877 63.81925 at 20iterations 0.9171284 30.35764 at 30iterations 0.4203088 13.47002 at 40iterations 0.1931015 6.286878 at 50iterations 8.8696852E-02 2.520413 at 60iterations 4.0631860E-02 1.304234 at 70iterations 1.8665781E-02 0.5459766 at 80iterations 8.5614054E-03 0.2765102 at 90iterations 3.9483765E-03 0.1181724 at 100iterations 1.8105835E-03 5.4225922E-02 at 110iterations 8.3525432E-04 2.3933411E-02 at 120iterations finished qdiffx linear iterations at : 15:03:12 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 8.3525432E-04 2.3933411E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 15:03:13 10.868u 0.463s 0:11.68 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 15:03:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.718802 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 2.718802 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3118 net assigned charge : 3.025009 assigned positive charge : 491.5638 centred at (gu) : 99.09336 86.64219 90.31592 assigned negative charge : -488.5401 centred at (gu) : 99.27992 86.78458 90.43855 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 199521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26120 grid for indexing accessible points = 1.400000 m= 99926 mr = 149404 m= 33391 mr = 82344 m= 7045 mr = 26723 m= 755 mr = 5263 m= 32 mr = 475 m= 0 mr = 15 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 6373 time to turn everything in is 1.770000 number of dielectric boundary points 76446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 24940 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) : 1.812535 object centre at (A) : 27.85450 1.431500 18.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0215974E-02 -0.2804935 midg,1,midg; midg,igrid,midg -2.4928604E-03 9.1313787E-02 1,midg,midg; igrid,midg,midg 0.4063348 0.2646763 gauss-seidel spectral radius is 0.9992456 estimated iterations to convergence 287 setup time was (sec) 2.100000 now iterating at: 15:03:15 rms-change max change #iterations 10.45901 312.0441 at 10iterations 6.064489 115.7041 at 20iterations 3.490380 69.26127 at 30iterations 2.008824 34.71696 at 40iterations 1.152228 20.70557 at 50iterations 0.6600998 11.98734 at 60iterations 0.3784848 6.339005 at 70iterations 0.2163796 3.761932 at 80iterations 0.1237318 2.373628 at 90iterations 7.0688553E-02 1.194061 at 100iterations 4.0479757E-02 0.7407227 at 110iterations 2.3197914E-02 0.3787498 at 120iterations 1.3237241E-02 0.2269974 at 130iterations 7.5841364E-03 0.1353455 at 140iterations 4.3518497E-03 7.6324463E-02 at 150iterations 2.4948169E-03 4.3186188E-02 at 160iterations 1.4350212E-03 2.4194717E-02 at 170iterations 8.2923286E-04 1.3387680E-02 at 180iterations finished qdiffx linear iterations at : 15:03:32 total time elapsed so far: 18.31000 # loops : 180 mean,max change (kT/e) : 8.2923286E-04 1.3387680E-02 energy calculations done at 18.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.49000 DelPhi exited at 15:03:32 18.494u 0.493s 0:19.27 98.4% 0+0k 0+0io 0pf+0w