Sun Oct 16 15:12:27 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 16 2011 at 15:12:27 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 = 2746 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: 0.6781340 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 0.6781340 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2599 net assigned charge : 5.500014 assigned positive charge : 416.4537 centred at (gu) : 90.47786 91.85542 90.79479 assigned negative charge : -410.9543 centred at (gu) : 90.16516 91.67455 90.88293 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8490 nv = 96 ne = 84 npr = 56151 no. pairs analyzed = 56151 no. exposed pairs = 3332 no. arc points = 23177 no. surface atoms = 1121 nbur = 1625 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4917 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.3200000 number of dielectric boundary points 4038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9833 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2475278E-08 -9.7123580E-09 midg,1,midg; midg,igrid,midg -2.6520281E-08 1.1645364E-07 1,midg,midg; igrid,midg,midg -7.6726657E-08 1.3296236E-07 gauss-seidel spectral radius is 0.9887368 estimated iterations to convergence 77 setup time was (sec) 0.5600000 now iterating at: 15:12:28 rms-change max change #iterations 0.1929335 24.82677 at 10iterations 2.2271268E-02 2.708799 at 20iterations 2.6231813E-03 0.3261337 at 30iterations 3.7178295E-04 5.0018311E-02 at 40iterations 7.6574004E-05 1.1360168E-02 at 50iterations finished qdiffx linear iterations at : 15:12:30 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.6574004E-05 1.1360168E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 15:12:31 3.452u 0.176s 0:03.91 92.5% 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 16 2011 at 15:12:31 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 = 2746 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: 2.034402 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 2.034402 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2599 net assigned charge : 5.500014 assigned positive charge : 416.4537 centred at (gu) : 91.43326 95.56563 92.38371 assigned negative charge : -410.9543 centred at (gu) : 90.49522 95.02336 92.64879 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 35109 mr = 64233 m= 6277 mr = 26635 m= 496 mr = 4164 m= 10 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2940 time to turn everything in is 0.6800000 number of dielectric boundary points 37220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20566 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) : 0.6781340 object centre at (A) : 18.01200 22.56200 67.25450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2925176E-02 -3.0287586E-02 midg,1,midg; midg,igrid,midg -5.7308611E-05 4.1249592E-02 1,midg,midg; igrid,midg,midg -2.9739650E-02 0.1035755 gauss-seidel spectral radius is 0.9988068 estimated iterations to convergence 229 setup time was (sec) 0.9600000 now iterating at: 15:12:32 rms-change max change #iterations 4.988948 246.7328 at 10iterations 2.440506 80.39632 at 20iterations 1.200153 38.67295 at 30iterations 0.5910362 15.88724 at 40iterations 0.2910534 7.922768 at 50iterations 0.1434191 3.803684 at 60iterations 7.0549481E-02 2.064165 at 70iterations 3.4725696E-02 1.094363 at 80iterations 1.7123867E-02 0.5000610 at 90iterations 8.4553352E-03 0.2234440 at 100iterations 4.1724355E-03 0.1313648 at 110iterations 2.0610183E-03 5.5641174E-02 at 120iterations finished qdiffx linear iterations at : 15:12:39 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.0610183E-03 5.5641174E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 15:12:39 7.820u 0.186s 0:08.31 96.2% 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 16 2011 at 15:12:39 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 = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.051603 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 3.051603 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2599 net assigned charge : 5.500014 assigned positive charge : 416.4537 centred at (gu) : 92.14953 98.34824 93.57572 assigned negative charge : -410.9543 centred at (gu) : 90.74275 97.53508 93.97295 start vw surface at 0.1400000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 208856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 110896 mr = 154423 m= 43465 mr = 92529 m= 11701 mr = 35792 m= 2105 mr = 9039 m= 208 mr = 1462 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 9906 time to turn everything in is 1.750000 number of dielectric boundary points 83870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 20792 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) : 2.034402 object centre at (A) : 18.01200 22.56200 67.25450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1554839 -0.3446979 midg,1,midg; midg,igrid,midg 5.8695037E-02 0.1605884 1,midg,midg; igrid,midg,midg -0.3301232 0.9324982 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.060000 now iterating at: 15:12:41 rms-change max change #iterations 11.22190 441.6166 at 10iterations 6.605912 173.9762 at 20iterations 3.889793 70.21554 at 30iterations 2.290194 48.69910 at 40iterations 1.348735 24.18513 at 50iterations 0.7894484 14.10619 at 60iterations 0.4628246 7.980625 at 70iterations 0.2709241 4.394355 at 80iterations 0.1585621 2.686674 at 90iterations 9.2803441E-02 1.605574 at 100iterations 5.4256663E-02 0.8938007 at 110iterations 3.1675771E-02 0.5104904 at 120iterations 1.8571146E-02 0.3175507 at 130iterations 1.0885877E-02 0.1751022 at 140iterations 6.4191013E-03 0.1079578 at 150iterations 3.7965020E-03 6.1344147E-02 at 160iterations 2.2705789E-03 4.3909073E-02 at 170iterations 1.3814821E-03 2.6535034E-02 at 180iterations finished qdiffx linear iterations at : 15:12:52 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.3814821E-03 2.6535034E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 15:12:53 12.945u 0.212s 0:13.48 97.5% 0+0k 0+0io 0pf+0w