Tue Oct 11 06:23:12 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+sph.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 = amb.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 Tue Oct 11 2011 at 06:23:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7181618 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 0.7181618 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.86182 89.91226 90.30791 assigned negative charge : -304.2972 centred at (gu) : 90.04726 89.89600 90.34402 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7167 nv = 96 ne = 84 npr = 40443 no. pairs analyzed = 40443 no. exposed pairs = 2470 no. arc points = 16802 no. surface atoms = 838 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4177 m= 6 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1614 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7466028E-08 6.2543307E-08 midg,1,midg; midg,igrid,midg 7.2497926E-08 8.9715471E-08 1,midg,midg; igrid,midg,midg 1.9766890E-07 -3.3016882E-08 gauss-seidel spectral radius is 0.9898865 estimated iterations to convergence 81 setup time was (sec) 0.5800000 now iterating at: 06:23:13 rms-change max change #iterations 0.2162201 32.19991 at 10iterations 2.7528543E-02 3.751389 at 20iterations 3.6248821E-03 0.5057297 at 30iterations 5.5490684E-04 7.8422546E-02 at 40iterations 1.1548748E-04 1.4478683E-02 at 50iterations finished qdiffx linear iterations at : 06:23:16 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.1548748E-04 1.4478683E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 06:23:17 4.086u 0.264s 0:04.71 92.1% 0+0k 0+0io 5pf+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 Tue Oct 11 2011 at 06:23:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.154485 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 2.154485 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.58515 89.73706 90.92402 assigned negative charge : -304.2972 centred at (gu) : 90.14172 89.68816 91.03219 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16802 grid for indexing accessible points = 1.400000 m= 30778 mr = 54238 m= 6103 mr = 23544 m= 593 mr = 4052 m= 13 mr = 296 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 31393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15328 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) : 0.7181618 object centre at (A) : 25.29600 21.51350 22.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9596371E-02 6.7247495E-02 midg,1,midg; midg,igrid,midg 6.7639090E-03 2.7713455E-02 1,midg,midg; igrid,midg,midg 5.1884890E-02 1.0973041E-02 gauss-seidel spectral radius is 0.9988568 estimated iterations to convergence 234 setup time was (sec) 0.9900000 now iterating at: 06:23:18 rms-change max change #iterations 4.647374 170.9301 at 10iterations 2.312138 76.75072 at 20iterations 1.161415 36.09506 at 30iterations 0.5793352 18.58204 at 40iterations 0.2902972 8.852075 at 50iterations 0.1450057 4.546970 at 60iterations 7.2818369E-02 2.613911 at 70iterations 3.6349509E-02 1.043119 at 80iterations 1.8198377E-02 0.5786438 at 90iterations 9.1744987E-03 0.2801881 at 100iterations 4.6374951E-03 0.1423222 at 110iterations 2.3671354E-03 6.8141937E-02 at 120iterations finished qdiffx linear iterations at : 06:23:26 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.3671354E-03 6.8141937E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 06:23:27 9.640u 0.317s 0:10.46 95.1% 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 Tue Oct 11 2011 at 06:23:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.231728 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 3.231728 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.37780 89.60553 91.38600 assigned negative charge : -304.2972 centred at (gu) : 90.21245 89.53230 91.54833 start vw surface at 0.1500000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 175462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16802 grid for indexing accessible points = 1.400000 m= 95915 mr = 130617 m= 39331 mr = 80220 m= 11554 mr = 32564 m= 2384 mr = 8963 m= 271 mr = 1689 m= 10 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 70690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 15432 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) : 2.154485 object centre at (A) : 25.29600 21.51350 22.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4982288 0.6178883 midg,1,midg; midg,igrid,midg 5.5206765E-04 0.2121592 1,midg,midg; igrid,midg,midg 0.3570365 0.2028170 gauss-seidel spectral radius is 0.9992984 estimated iterations to convergence 298 setup time was (sec) 2.600000 now iterating at: 06:23:30 rms-change max change #iterations 10.26740 450.6276 at 10iterations 6.095603 133.0143 at 20iterations 3.604202 81.63976 at 30iterations 2.126870 44.80413 at 40iterations 1.252408 22.87990 at 50iterations 0.7384309 12.96466 at 60iterations 0.4347124 8.254923 at 70iterations 0.2551665 4.329795 at 80iterations 0.1495383 2.873308 at 90iterations 8.8110976E-02 1.639495 at 100iterations 5.1812850E-02 0.9577675 at 110iterations 3.0576264E-02 0.5399246 at 120iterations 1.8209029E-02 0.3451424 at 130iterations 1.0971506E-02 0.1996994 at 140iterations 6.8014399E-03 0.1260300 at 150iterations 4.3630684E-03 8.8687897E-02 at 160iterations 2.9587853E-03 5.5667877E-02 at 170iterations 2.1287694E-03 3.8761139E-02 at 180iterations finished qdiffx linear iterations at : 06:23:44 total time elapsed so far: 16.54000 # loops : 180 mean,max change (kT/e) : 2.1287694E-03 3.8761139E-02 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.72000 DelPhi exited at 06:23:45 16.725u 0.316s 0:17.51 97.2% 0+0k 0+0io 0pf+0w