Mon Oct 10 10:19:33 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 10:19:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2801 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5771164 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 0.5771164 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.01402 assigned positive charge : 413.2130 centred at (gu) : 91.99516 91.81792 86.83149 assigned negative charge : -401.1995 centred at (gu) : 92.08987 91.85467 86.62502 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6376 nv = 96 ne = 84 npr = 53684 no. pairs analyzed = 53684 no. exposed pairs = 4084 no. arc points = 29928 no. surface atoms = 1355 nbur = 1446 mkacc time = 0.1100000 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= 323 mr = 2875 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2993 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8386440E-09 2.9200822E-09 midg,1,midg; midg,igrid,midg 2.0824129E-09 2.8081379E-09 1,midg,midg; igrid,midg,midg 2.6280795E-09 1.2428504E-09 gauss-seidel spectral radius is 0.9845074 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 10:19:34 rms-change max change #iterations 9.1302760E-02 17.86102 at 10iterations 6.9638751E-03 1.150070 at 20iterations 5.5639405E-04 8.4144592E-02 at 30iterations 4.9760383E-05 7.5073242E-03 at 40iterations 6.6953803E-06 8.5783005E-04 at 50iterations finished qdiffx linear iterations at : 10:19:37 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 6.6953803E-06 8.5783005E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 10:19:37 3.304u 0.193s 0:03.88 89.9% 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 Mon Oct 10 2011 at 10:19:37 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2801 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.731349 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 1.731349 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.01402 assigned positive charge : 413.2130 centred at (gu) : 95.98465 95.45320 80.49383 assigned negative charge : -401.1995 centred at (gu) : 96.26937 95.56380 79.87477 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 68270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29928 grid for indexing accessible points = 1.400000 m= 22375 mr = 42404 m= 2965 mr = 14687 m= 116 mr = 1382 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 35241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20618 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) : 0.5771164 object centre at (A) : 8.998000 15.67050 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3374291E-04 1.3846654E-02 midg,1,midg; midg,igrid,midg 1.8236717E-02 2.8458504E-02 1,midg,midg; igrid,midg,midg -6.9053858E-03 1.1832814E-02 gauss-seidel spectral radius is 0.9983840 estimated iterations to convergence 197 setup time was (sec) 0.7700000 now iterating at: 10:19:38 rms-change max change #iterations 3.542520 147.2035 at 10iterations 1.526756 65.09283 at 20iterations 0.6668904 23.84435 at 30iterations 0.2914180 10.48240 at 40iterations 0.1266896 4.380335 at 50iterations 5.5528622E-02 1.876876 at 60iterations 2.4158068E-02 0.9078102 at 70iterations 1.0563343E-02 0.3842163 at 80iterations 4.6036141E-03 0.1624413 at 90iterations 2.0196277E-03 7.6339722E-02 at 100iterations 8.8281924E-04 3.4975052E-02 at 110iterations 3.8692649E-04 1.4973164E-02 at 120iterations finished qdiffx linear iterations at : 10:19:45 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 3.8692649E-04 1.4973164E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 10:19:45 7.424u 0.225s 0:07.95 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 Mon Oct 10 2011 at 10:19:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2801 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.597024 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 2.597024 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.01402 assigned positive charge : 413.2130 centred at (gu) : 98.97692 98.17973 75.74072 assigned negative charge : -401.1995 centred at (gu) : 99.40412 98.34566 74.81213 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 158024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29928 grid for indexing accessible points = 1.400000 m= 72882 mr = 104751 m= 24392 mr = 55433 m= 4792 mr = 17695 m= 410 mr = 2973 m= 20 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 79505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 21230 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) : 1.731349 object centre at (A) : 8.998000 15.67050 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1878962E-03 0.1465184 midg,1,midg; midg,igrid,midg 0.2970588 0.3433282 1,midg,midg; igrid,midg,midg -0.3398722 0.2194920 gauss-seidel spectral radius is 0.9992020 estimated iterations to convergence 280 setup time was (sec) 1.480000 now iterating at: 10:19:47 rms-change max change #iterations 9.180515 290.6017 at 10iterations 5.364518 153.2340 at 20iterations 3.089420 87.09379 at 30iterations 1.773502 61.91909 at 40iterations 1.012052 24.19810 at 50iterations 0.5758121 14.88171 at 60iterations 0.3266232 8.006726 at 70iterations 0.1849803 4.095254 at 80iterations 0.1043250 2.196621 at 90iterations 5.8894496E-02 1.347957 at 100iterations 3.3233467E-02 0.6576004 at 110iterations 1.8758144E-02 0.4636760 at 120iterations 1.0565011E-02 0.2165184 at 130iterations 5.9364918E-03 0.1281815 at 140iterations 3.3395081E-03 7.9123497E-02 at 150iterations 1.8798434E-03 4.1792870E-02 at 160iterations 1.0604253E-03 2.1434784E-02 at 170iterations 5.9572281E-04 1.1430740E-02 at 180iterations finished qdiffx linear iterations at : 10:19:57 total time elapsed so far: 10.93000 # loops : 180 mean,max change (kT/e) : 5.9572281E-04 1.1430740E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 10:19:57 11.116u 0.158s 0:11.63 96.8% 0+0k 0+0io 0pf+0w