Mon Oct 10 09:46:33 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 09:46:33 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: TYR 183 has a net charge of -0.0260 !!! WARNING: HIT 235 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5699739 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): 114.7780 177.2370 ymin,ymax (A): -43.15800 10.43000 zmin,zma (A): 50.51900 106.0040 x,y,z range (A): 62.45900 53.58800 55.48500 scale (grids/A): 0.5699739 object centre (A): 146.0075 -16.36400 78.26150 number of atom coordinates read : 2881 total number of charged atoms : 2732 net assigned charge : 7.988016 assigned positive charge : 425.2699 centred at (gu) : 89.85126 88.85896 88.56889 assigned negative charge : -417.2824 centred at (gu) : 89.92342 88.96053 88.44099 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6277 nv = 96 ne = 84 npr = 55729 no. pairs analyzed = 55729 no. exposed pairs = 4346 no. arc points = 31257 no. surface atoms = 1448 nbur = 1433 mkacc time = 0.1400000 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= 328 mr = 2707 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3203 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8021 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.8823771E-10 2.1993452E-09 midg,1,midg; midg,igrid,midg 3.5504610E-09 -1.9868839E-10 1,midg,midg; igrid,midg,midg 2.3631681E-09 1.5938735E-10 gauss-seidel spectral radius is 0.9841286 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 09:46:34 rms-change max change #iterations 8.9105718E-02 15.73434 at 10iterations 6.5660924E-03 1.221166 at 20iterations 4.9014704E-04 9.2137337E-02 at 30iterations 3.9085506E-05 5.9738159E-03 at 40iterations 4.2513257E-06 5.8364868E-04 at 50iterations finished qdiffx linear iterations at : 09:46:38 total time elapsed so far: 5.130000 # loops : 50 mean,max change (kT/e) : 4.2513257E-06 5.8364868E-04 energy calculations done at 5.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 09:46:39 5.296u 0.479s 0:06.03 95.5% 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 Mon Oct 10 2011 at 09:46:39 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: TYR 183 has a net charge of -0.0260 !!! WARNING: HIT 235 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.709922 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): 114.7780 177.2370 ymin,ymax (A): -43.15800 10.43000 zmin,zma (A): 50.51900 106.0040 x,y,z range (A): 62.45900 53.58800 55.48500 scale (grids/A): 1.709922 object centre (A): 146.0075 -16.36400 78.26150 number of atom coordinates read : 2881 total number of charged atoms : 2732 net assigned charge : 7.988016 assigned positive charge : 425.2699 centred at (gu) : 89.55319 86.57629 85.70580 assigned negative charge : -417.2824 centred at (gu) : 89.77007 86.88120 85.32260 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31257 grid for indexing accessible points = 1.400000 m= 21522 mr = 39737 m= 3061 mr = 13854 m= 127 mr = 1479 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.6100000 number of dielectric boundary points 35973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21156 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) : 0.5699739 object centre at (A) : 146.0075 -16.36400 78.26150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4048879E-03 2.3017682E-02 midg,1,midg; midg,igrid,midg 1.7833756E-02 4.0913299E-03 1,midg,midg; igrid,midg,midg 2.2228323E-02 1.2813169E-02 gauss-seidel spectral radius is 0.9983655 estimated iterations to convergence 196 setup time was (sec) 1.000000 now iterating at: 09:46:40 rms-change max change #iterations 3.587205 172.9881 at 10iterations 1.552388 56.57053 at 20iterations 0.6719480 27.46771 at 30iterations 0.2910350 10.75887 at 40iterations 0.1257635 4.987488 at 50iterations 5.4873828E-02 2.147057 at 60iterations 2.3731364E-02 0.8449783 at 70iterations 1.0292789E-02 0.3819962 at 80iterations 4.4807913E-03 0.1778870 at 90iterations 1.9592866E-03 6.5560341E-02 at 100iterations 8.4807834E-04 3.2325745E-02 at 110iterations 3.6892956E-04 1.3290405E-02 at 120iterations finished qdiffx linear iterations at : 09:46:52 total time elapsed so far: 12.73000 # loops : 120 mean,max change (kT/e) : 3.6892956E-04 1.3290405E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 09:46:52 12.890u 0.540s 0:13.72 97.8% 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 09:46:52 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 !!! WARNING: TYR 183 has a net charge of -0.0260 !!! WARNING: HIT 235 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.564883 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): 114.7780 177.2370 ymin,ymax (A): -43.15800 10.43000 zmin,zma (A): 50.51900 106.0040 x,y,z range (A): 62.45900 53.58800 55.48500 scale (grids/A): 2.564883 object centre (A): 146.0075 -16.36400 78.26150 number of atom coordinates read : 2881 total number of charged atoms : 2732 net assigned charge : 7.988016 assigned positive charge : 425.2699 centred at (gu) : 89.32963 84.86441 83.55887 assigned negative charge : -417.2824 centred at (gu) : 89.65501 85.32190 82.98389 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 153233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31257 grid for indexing accessible points = 1.400000 m= 69272 mr = 98376 m= 23796 mr = 51389 m= 4956 mr = 17396 m= 483 mr = 3157 m= 14 mr = 220 m= 0 mr = 2 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 1.530000 number of dielectric boundary points 81214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 21845 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) : 1.709922 object centre at (A) : 146.0075 -16.36400 78.26150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1166941 0.2961661 midg,1,midg; midg,igrid,midg 0.2137625 8.4911451E-02 1,midg,midg; igrid,midg,midg 0.1939217 0.1830715 gauss-seidel spectral radius is 0.9992107 estimated iterations to convergence 281 setup time was (sec) 1.910000 now iterating at: 09:46:55 rms-change max change #iterations 9.374537 291.9188 at 10iterations 5.541529 156.2166 at 20iterations 3.231734 84.19892 at 30iterations 1.873029 48.82947 at 40iterations 1.072651 26.06279 at 50iterations 0.6138043 16.43880 at 60iterations 0.3494529 7.949426 at 70iterations 0.1984256 4.818993 at 80iterations 0.1128107 2.617950 at 90iterations 6.3897707E-02 1.499913 at 100iterations 3.6193829E-02 0.7574577 at 110iterations 2.0456469E-02 0.4808183 at 120iterations 1.1563996E-02 0.2430649 at 130iterations 6.5261386E-03 0.1357670 at 140iterations 3.6772238E-03 7.2715759E-02 at 150iterations 2.0765206E-03 5.1895142E-02 at 160iterations 1.1715003E-03 2.5973797E-02 at 170iterations 6.5985764E-04 1.3412476E-02 at 180iterations finished qdiffx linear iterations at : 09:47:14 total time elapsed so far: 21.18000 # loops : 180 mean,max change (kT/e) : 6.5985764E-04 1.3412476E-02 energy calculations done at 21.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.34000 DelPhi exited at 09:47:15 21.347u 0.564s 0:22.21 98.6% 0+0k 0+0io 0pf+0w