Sun Oct 9 13:19:46 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 Sun Oct 9 2011 at 13:19:46 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 = 2389 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: 0.6972600 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 0.6972600 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 363.1021 centred at (gu) : 89.75102 91.37283 90.30429 assigned negative charge : -359.6026 centred at (gu) : 89.77595 91.55817 90.35661 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7908 nv = 96 ne = 84 npr = 47882 no. pairs analyzed = 47882 no. exposed pairs = 2985 no. arc points = 21118 no. surface atoms = 1003 nbur = 1386 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4438 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5242199E-08 7.3728901E-10 midg,1,midg; midg,igrid,midg 8.1298445E-08 -8.0951843E-08 1,midg,midg; igrid,midg,midg 3.7531318E-08 1.2657789E-08 gauss-seidel spectral radius is 0.9893157 estimated iterations to convergence 79 setup time was (sec) 0.4900000 now iterating at: 13:19:47 rms-change max change #iterations 0.2016290 30.43378 at 10iterations 2.4368688E-02 3.390545 at 20iterations 3.4798945E-03 0.4299927 at 30iterations 7.9678750E-04 0.1387901 at 40iterations 2.6853825E-04 4.2778015E-02 at 50iterations finished qdiffx linear iterations at : 13:19:49 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 2.6853825E-04 4.2778015E-02 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 13:19:50 3.211u 0.145s 0:03.64 92.0% 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 Sun Oct 9 2011 at 13:19:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 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: 2.091780 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 2.091780 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 363.1021 centred at (gu) : 89.25259 94.11803 90.91257 assigned negative charge : -359.6026 centred at (gu) : 89.32768 94.67443 91.06960 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21118 grid for indexing accessible points = 1.400000 m= 32890 mr = 58453 m= 6255 mr = 24717 m= 607 mr = 4087 m= 13 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 36089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17832 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) : 0.6972600 object centre at (A) : 18.81150 47.46650 63.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7072148E-02 2.3461539E-04 midg,1,midg; midg,igrid,midg 1.6974572E-02 -6.8697825E-02 1,midg,midg; igrid,midg,midg 6.8349697E-02 -1.0881741E-02 gauss-seidel spectral radius is 0.9988410 estimated iterations to convergence 232 setup time was (sec) 0.9100000 now iterating at: 13:19:51 rms-change max change #iterations 4.945107 221.4198 at 10iterations 2.448140 85.57407 at 20iterations 1.217779 40.70547 at 30iterations 0.6041482 18.21526 at 40iterations 0.3007993 8.975052 at 50iterations 0.1495896 4.402599 at 60iterations 7.4759141E-02 2.413417 at 70iterations 3.7343476E-02 1.098767 at 80iterations 1.8723100E-02 0.5267487 at 90iterations 9.4961086E-03 0.2505474 at 100iterations 4.8848242E-03 0.1564255 at 110iterations 2.6104278E-03 8.1344128E-02 at 120iterations finished qdiffx linear iterations at : 13:19:57 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 2.6104278E-03 8.1344128E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 13:19:57 7.062u 0.161s 0:07.51 96.1% 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 Sun Oct 9 2011 at 13:19:57 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 = 2389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 3.137670 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 3.137670 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 363.1021 centred at (gu) : 88.87881 96.17708 91.36858 assigned negative charge : -359.6026 centred at (gu) : 88.99147 97.01138 91.60436 start vw surface at 0.1800000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 193228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21118 grid for indexing accessible points = 1.400000 m= 102564 mr = 140767 m= 41652 mr = 84708 m= 11665 mr = 34079 m= 2486 mr = 8955 m= 311 mr = 1793 m= 7 mr = 189 m= 0 mr = 2 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 81420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 17984 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) : 2.091780 object centre at (A) : 18.81150 47.46650 63.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5323133 -0.1376241 midg,1,midg; midg,igrid,midg 0.3511887 -0.7431027 1,midg,midg; igrid,midg,midg 0.7218086 -0.4057494 gauss-seidel spectral radius is 0.9993036 estimated iterations to convergence 299 setup time was (sec) 2.150000 now iterating at: 13:19:59 rms-change max change #iterations 10.94892 407.1576 at 10iterations 6.496522 159.8107 at 20iterations 3.838403 76.19379 at 30iterations 2.267896 52.43541 at 40iterations 1.339048 21.71239 at 50iterations 0.7875084 14.27645 at 60iterations 0.4634379 8.248280 at 70iterations 0.2723397 4.525846 at 80iterations 0.1597000 2.812114 at 90iterations 9.3975484E-02 1.617090 at 100iterations 5.5192932E-02 0.8903885 at 110iterations 3.2580797E-02 0.5271454 at 120iterations 1.9386383E-02 0.3495522 at 130iterations 1.1701889E-02 0.1927719 at 140iterations 7.2559244E-03 0.1299286 at 150iterations 4.6936306E-03 8.8634491E-02 at 160iterations 3.2044938E-03 6.5734863E-02 at 170iterations 2.3525648E-03 5.4218292E-02 at 180iterations finished qdiffx linear iterations at : 13:20:09 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 2.3525648E-03 5.4218292E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 13:20:09 11.713u 0.191s 0:12.18 97.7% 0+0k 0+0io 0pf+0w