Mon Oct 10 17:00:51 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 Mon Oct 10 2011 at 17:00:51 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5100725 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 0.5100725 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4407 net assigned charge : 5.706027 assigned positive charge : 697.8676 centred at (gu) : 90.20763 90.42032 88.25837 assigned negative charge : -692.1660 centred at (gu) : 90.09173 90.43732 88.23724 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7789 nv = 96 ne = 84 npr = 93322 no. pairs analyzed = 93322 no. exposed pairs = 6032 no. arc points = 41779 no. surface atoms = 2012 nbur = 2644 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 = 1.680000 m= 268 mr = 3991 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3989 ## 571 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10234 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1611398E-11 8.3609702E-11 midg,1,midg; midg,igrid,midg 1.0852681E-10 4.1826816E-11 1,midg,midg; igrid,midg,midg -1.9732238E-10 3.7930042E-10 gauss-seidel spectral radius is 0.9803399 estimated iterations to convergence 59 setup time was (sec) 0.4700000 now iterating at: 17:00:51 rms-change max change #iterations 6.6460751E-02 9.365505 at 10iterations 3.9282334E-03 0.6536179 at 20iterations 4.5659975E-04 6.2573433E-02 at 30iterations 1.6856763E-04 2.4671316E-02 at 40iterations 7.2786475E-05 1.1149645E-02 at 50iterations finished qdiffx linear iterations at : 17:00:54 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.2786475E-05 1.1149645E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:00:55 3.485u 0.210s 0:04.07 90.6% 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 Mon Oct 10 2011 at 17:00:55 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.530218 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 1.530218 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4407 net assigned charge : 5.706027 assigned positive charge : 697.8676 centred at (gu) : 90.62160 91.25948 84.77380 assigned negative charge : -692.1660 centred at (gu) : 90.27505 91.31166 84.71149 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25310 mr = 60452 m= 2149 mr = 16580 m= 34 mr = 867 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 37873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 575 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 33060 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) : 0.5100725 object centre at (A) : 9.272001 1.625000 30.92700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7208459E-03 1.8569332E-02 midg,1,midg; midg,igrid,midg 2.7818021E-03 -7.5729075E-03 1,midg,midg; igrid,midg,midg -1.8434842E-03 1.1210663E-02 gauss-seidel spectral radius is 0.9981027 estimated iterations to convergence 182 setup time was (sec) 0.6700000 now iterating at: 17:00:56 rms-change max change #iterations 3.728501 175.6860 at 10iterations 1.524736 52.23522 at 20iterations 0.6242481 22.23253 at 30iterations 0.2564031 9.097897 at 40iterations 0.1049819 3.458203 at 50iterations 4.2977188E-02 1.359173 at 60iterations 1.7601231E-02 0.5633869 at 70iterations 7.2563267E-03 0.2279968 at 80iterations 2.9889862E-03 9.8121643E-02 at 90iterations 1.2417623E-03 3.7175179E-02 at 100iterations 5.2612857E-04 1.8348694E-02 at 110iterations 2.3741771E-04 9.2012882E-03 at 120iterations finished qdiffx linear iterations at : 17:01:03 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 2.3741771E-04 9.2012882E-03 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 17:01:04 8.457u 0.232s 0:09.75 89.0% 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 Mon Oct 10 2011 at 17:01:05 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.295326 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 2.295326 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4407 net assigned charge : 5.706027 assigned positive charge : 697.8676 centred at (gu) : 90.93185 91.88885 82.16042 assigned negative charge : -692.1660 centred at (gu) : 90.41255 91.96732 82.06721 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 205558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91425 mr = 148468 m= 22545 mr = 70919 m= 3100 mr = 15893 m= 164 mr = 1878 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 85572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 35157 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) : 1.530218 object centre at (A) : 9.272001 1.625000 30.92700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1294629 0.4797326 midg,1,midg; midg,igrid,midg -2.0994307E-02 -0.2143779 1,midg,midg; igrid,midg,midg -2.3189120E-02 0.1574323 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.290000 now iterating at: 17:01:06 rms-change max change #iterations 10.18092 305.8336 at 10iterations 5.832400 147.0869 at 20iterations 3.319249 80.13736 at 30iterations 1.871856 56.37259 at 40iterations 1.055113 24.04622 at 50iterations 0.5912607 13.26923 at 60iterations 0.3308020 6.883379 at 70iterations 0.1853533 4.029121 at 80iterations 0.1032823 2.199377 at 90iterations 5.7513364E-02 1.221565 at 100iterations 3.2041296E-02 0.5957870 at 110iterations 1.7839668E-02 0.3752441 at 120iterations 9.9097583E-03 0.2190156 at 130iterations 5.5291527E-03 0.1021614 at 140iterations 3.0764062E-03 5.9970856E-02 at 150iterations 1.7231805E-03 3.5516739E-02 at 160iterations 9.7417325E-04 2.2129059E-02 at 170iterations 5.5973540E-04 1.1096716E-02 at 180iterations finished qdiffx linear iterations at : 17:01:19 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 5.5973540E-04 1.1096716E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 17:01:20 14.018u 0.287s 0:14.99 95.3% 0+0k 0+0io 0pf+0w