Mon Oct 10 14:12:38 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 14:12:38 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5769760 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 0.5769760 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1972 total number of charged atoms : 1830 net assigned charge : 2.752003 assigned positive charge : 292.2269 centred at (gu) : 90.06404 90.70604 90.65081 assigned negative charge : -289.4753 centred at (gu) : 90.06779 90.89445 90.64958 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4333 nv = 96 ne = 84 npr = 40596 no. pairs analyzed = 40596 no. exposed pairs = 2532 no. arc points = 17608 no. surface atoms = 857 nbur = 1115 mkacc time = 6.0000002E-02 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 = 1.484000 m= 174 mr = 2279 m= 0 mr = 9 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.1600000 number of dielectric boundary points 2219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1764 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7156429E-10 6.7168954E-10 midg,1,midg; midg,igrid,midg 2.4959879E-09 -2.2980780E-09 1,midg,midg; igrid,midg,midg 6.0230154E-10 5.2146915E-10 gauss-seidel spectral radius is 0.9844132 estimated iterations to convergence 66 setup time was (sec) 0.3500000 now iterating at: 14:12:38 rms-change max change #iterations 7.9526983E-02 17.24969 at 10iterations 6.0170470E-03 1.013424 at 20iterations 4.6732186E-04 8.7512970E-02 at 30iterations 3.6246034E-05 7.8315735E-03 at 40iterations 2.7319043E-06 5.4168701E-04 at 50iterations finished qdiffx linear iterations at : 14:12:41 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.7319043E-06 5.4168701E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:12:42 3.293u 0.159s 0:04.06 84.7% 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 14:12:42 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.730928 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 1.730928 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1972 total number of charged atoms : 1830 net assigned charge : 2.752003 assigned positive charge : 292.2269 centred at (gu) : 90.19226 92.11796 91.95216 assigned negative charge : -289.4753 centred at (gu) : 90.20354 92.68354 91.94914 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17608 grid for indexing accessible points = 1.400000 m= 15447 mr = 32024 m= 1675 mr = 11237 m= 52 mr = 913 m= 0 mr = 1 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 20495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 14235 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) : 0.5769760 object centre at (A) : 13.46700 29.09600 36.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9541156E-02 2.2732396E-02 midg,1,midg; midg,igrid,midg 7.9966364E-03 -1.1393642E-02 1,midg,midg; igrid,midg,midg -2.2244880E-03 -3.2275009E-03 gauss-seidel spectral radius is 0.9982710 estimated iterations to convergence 191 setup time was (sec) 0.4400000 now iterating at: 14:12:43 rms-change max change #iterations 2.953851 138.4235 at 10iterations 1.257314 56.99222 at 20iterations 0.5355536 22.78787 at 30iterations 0.2273642 9.564056 at 40iterations 9.6517429E-02 3.978521 at 50iterations 4.1138668E-02 1.621952 at 60iterations 1.7494909E-02 0.7036238 at 70iterations 7.4579529E-03 0.2878673 at 80iterations 3.1611728E-03 0.1185188 at 90iterations 1.3430108E-03 5.2820206E-02 at 100iterations 5.7241757E-04 2.2865295E-02 at 110iterations 2.4367339E-04 9.5672607E-03 at 120iterations finished qdiffx linear iterations at : 14:12:49 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.4367339E-04 9.5672607E-03 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 14:12:50 7.395u 0.193s 0:08.16 92.8% 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 14:12:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1972 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.596392 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 2.596392 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1972 total number of charged atoms : 1830 net assigned charge : 2.752003 assigned positive charge : 292.2269 centred at (gu) : 90.28842 93.17705 92.92818 assigned negative charge : -289.4753 centred at (gu) : 90.30532 94.02528 92.92370 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 109832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17608 grid for indexing accessible points = 1.400000 m= 51946 mr = 77770 m= 16404 mr = 42126 m= 2855 mr = 13094 m= 159 mr = 1976 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 46175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14632 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) : 1.730928 object centre at (A) : 13.46700 29.09600 36.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1754092 0.3439254 midg,1,midg; midg,igrid,midg 8.4886432E-02 -0.1680128 1,midg,midg; igrid,midg,midg -4.7315311E-02 -5.4853585E-02 gauss-seidel spectral radius is 0.9991335 estimated iterations to convergence 268 setup time was (sec) 0.8100000 now iterating at: 14:12:51 rms-change max change #iterations 7.403943 243.9966 at 10iterations 4.103189 136.2611 at 20iterations 2.257461 57.47504 at 30iterations 1.242288 32.18673 at 40iterations 0.6826399 16.66722 at 50iterations 0.3743222 8.266494 at 60iterations 0.2051404 4.651934 at 70iterations 0.1124880 2.868706 at 80iterations 6.1506227E-02 1.395805 at 90iterations 3.3672448E-02 0.8511854 at 100iterations 1.8444646E-02 0.4800386 at 110iterations 1.0083545E-02 0.2263334 at 120iterations 5.5148611E-03 0.1210594 at 130iterations 3.0296117E-03 6.9772720E-02 at 140iterations 1.6579307E-03 3.9335251E-02 at 150iterations 9.0527098E-04 2.0202637E-02 at 160iterations 4.9629738E-04 1.1070251E-02 at 170iterations 2.7145282E-04 6.8332553E-03 at 180iterations finished qdiffx linear iterations at : 14:13:02 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 2.7145282E-04 6.8332553E-03 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 14:13:02 11.628u 0.185s 0:12.13 97.2% 0+0k 0+0io 0pf+0w