Sat Oct 15 15:16:32 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 15 2011 at 15:16:32 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5549234 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 0.5549234 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3797 net assigned charge : 10.53902 assigned positive charge : 612.1395 centred at (gu) : 90.67551 90.31222 92.92403 assigned negative charge : -601.6042 centred at (gu) : 90.73856 90.26974 93.02413 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 76475 no. pairs analyzed = 76475 no. exposed pairs = 5477 no. arc points = 38829 no. surface atoms = 1797 nbur = 2161 mkacc time = 0.2600000 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 = 1.568000 m= 335 mr = 3806 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3990 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 10408 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0850056E-09 -6.7436978E-10 midg,1,midg; midg,igrid,midg 4.0509548E-10 1.5986581E-09 1,midg,midg; igrid,midg,midg 1.4730398E-09 2.0085382E-10 gauss-seidel spectral radius is 0.9833338 estimated iterations to convergence 64 setup time was (sec) 0.8500000 now iterating at: 15:16:34 rms-change max change #iterations 9.1349147E-02 13.71753 at 10iterations 6.4688730E-03 0.9386644 at 20iterations 5.8780785E-04 9.2376709E-02 at 30iterations 1.1096439E-04 1.6151428E-02 at 40iterations 3.2322652E-05 5.1994324E-03 at 50iterations finished qdiffx linear iterations at : 15:16:48 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 3.2322652E-05 5.1994324E-03 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.420000 DelPhi exited at 15:16:50 5.420u 0.466s 0:18.39 31.9% 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 15 2011 at 15:16:50 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.664770 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 1.664770 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3797 net assigned charge : 10.53902 assigned positive charge : 612.1395 centred at (gu) : 92.02489 90.93484 98.77038 assigned negative charge : -601.6042 centred at (gu) : 92.21515 90.80869 99.07172 start vw surface at 0.2100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 87116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26827 mr = 56748 m= 2794 mr = 17387 m= 70 mr = 1206 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 41464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 29159 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) : 0.5549234 object centre at (A) : 15.90750 55.56750 47.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8165201E-02 7.0838463E-03 midg,1,midg; midg,igrid,midg 1.7300243E-02 2.0914618E-02 1,midg,midg; igrid,midg,midg 3.4813754E-02 -5.5922209E-03 gauss-seidel spectral radius is 0.9983559 estimated iterations to convergence 196 setup time was (sec) 1.300000 now iterating at: 15:16:52 rms-change max change #iterations 4.113241 202.4824 at 10iterations 1.774595 71.04985 at 20iterations 0.7701075 24.78838 at 30iterations 0.3337334 11.15920 at 40iterations 0.1449890 5.265308 at 50iterations 6.3002042E-02 2.402303 at 60iterations 2.7354648E-02 0.8321953 at 70iterations 1.1864869E-02 0.3693466 at 80iterations 5.1903254E-03 0.1784306 at 90iterations 2.2643150E-03 7.5378418E-02 at 100iterations 9.9365762E-04 3.2758713E-02 at 110iterations 4.3973984E-04 1.4113426E-02 at 120iterations finished qdiffx linear iterations at : 15:17:06 total time elapsed so far: 12.55000 # loops : 120 mean,max change (kT/e) : 4.3973984E-04 1.4113426E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 15:17:07 12.767u 0.487s 0:16.81 78.7% 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 Sat Oct 15 2011 at 15:17:07 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.497155 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 2.497155 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3797 net assigned charge : 10.53902 assigned positive charge : 612.1395 centred at (gu) : 93.03704 91.40183 103.1549 assigned negative charge : -601.6042 centred at (gu) : 93.32262 91.21288 103.6074 start vw surface at 0.2000000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 202212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91726 mr = 139932 m= 26207 mr = 69832 m= 4209 mr = 18696 m= 285 mr = 2551 m= 4 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.290000 number of dielectric boundary points 93533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 30336 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) : 1.664770 object centre at (A) : 15.90750 55.56750 47.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1640320 7.7339619E-02 midg,1,midg; midg,igrid,midg 0.1672573 0.3432596 1,midg,midg; igrid,midg,midg 0.4853327 -9.3117289E-02 gauss-seidel spectral radius is 0.9992132 estimated iterations to convergence 281 setup time was (sec) 2.700000 now iterating at: 15:17:11 rms-change max change #iterations 10.70169 336.4287 at 10iterations 6.205832 141.1073 at 20iterations 3.575377 80.11475 at 30iterations 2.045656 42.45705 at 40iterations 1.170294 24.37184 at 50iterations 0.6669870 14.11336 at 60iterations 0.3793699 8.135701 at 70iterations 0.2157134 4.558769 at 80iterations 0.1222558 2.366987 at 90iterations 6.9214903E-02 1.289650 at 100iterations 3.9206114E-02 0.7049809 at 110iterations 2.2190403E-02 0.4133072 at 120iterations 1.2559530E-02 0.2243462 at 130iterations 7.0929090E-03 0.1327209 at 140iterations 4.0134476E-03 7.1272731E-02 at 150iterations 2.2777130E-03 4.4130325E-02 at 160iterations 1.2925522E-03 2.4496078E-02 at 170iterations 7.3720468E-04 1.3282776E-02 at 180iterations finished qdiffx linear iterations at : 15:17:32 total time elapsed so far: 22.13000 # loops : 180 mean,max change (kT/e) : 7.3720468E-04 1.3282776E-02 energy calculations done at 22.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.35000 DelPhi exited at 15:17:33 22.356u 0.553s 0:25.66 89.2% 0+0k 0+0io 0pf+0w