Sat Oct 8 11:37:20 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 8 2011 at 11:37:20 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 = 4086 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5148228 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 0.5148228 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.985960 assigned positive charge : 614.0102 centred at (gu) : 88.69832 89.73508 90.55657 assigned negative charge : -621.9982 centred at (gu) : 88.74866 89.79625 90.60040 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6708 nv = 96 ne = 84 npr = 86179 no. pairs analyzed = 86179 no. exposed pairs = 4668 no. arc points = 31427 no. surface atoms = 1609 nbur = 2477 mkacc time = 0.1500000 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 = 1.652000 m= 210 mr = 3703 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2900000 number of dielectric boundary points 3212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3185 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8432015E-11 -2.9697658E-10 midg,1,midg; midg,igrid,midg 2.7996107E-11 -2.8411476E-10 1,midg,midg; igrid,midg,midg -1.4773195E-12 -1.9638287E-10 gauss-seidel spectral radius is 0.9806436 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 11:37:21 rms-change max change #iterations 6.3857399E-02 13.47803 at 10iterations 4.2160116E-03 0.7460785 at 20iterations 6.0179492E-04 8.9434624E-02 at 30iterations 1.6167411E-04 2.7046204E-02 at 40iterations 4.7423997E-05 8.2283020E-03 at 50iterations finished qdiffx linear iterations at : 11:37:24 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 4.7423997E-05 8.2283020E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 11:37:25 4.048u 0.237s 0:04.78 89.3% 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 8 2011 at 11:37:25 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 = 4086 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.544469 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 1.544469 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.985960 assigned positive charge : 614.0102 centred at (gu) : 86.09379 89.20434 91.66864 assigned negative charge : -621.9982 centred at (gu) : 86.24557 89.38809 91.80072 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 76500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31427 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22332 mr = 54527 m= 2005 mr = 15390 m= 33 mr = 889 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 736 time to turn everything in is 0.3800000 number of dielectric boundary points 30064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 417 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 29680 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) : 0.5148228 object centre at (A) : 30.99100 14.66550 12.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1013357E-03 -1.1373015E-02 midg,1,midg; midg,igrid,midg -3.8015128E-03 -9.2861438E-03 1,midg,midg; igrid,midg,midg 1.3280809E-02 -5.9685698E-03 gauss-seidel spectral radius is 0.9980585 estimated iterations to convergence 180 setup time was (sec) 0.6500000 now iterating at: 11:37:26 rms-change max change #iterations 3.548116 196.6941 at 10iterations 1.428982 53.69159 at 20iterations 0.5800795 19.22902 at 30iterations 0.2357092 8.556229 at 40iterations 9.5486991E-02 3.369377 at 50iterations 3.8856689E-02 1.428177 at 60iterations 1.5864592E-02 0.5127945 at 70iterations 6.5401169E-03 0.2359619 at 80iterations 2.7375419E-03 8.9441299E-02 at 90iterations 1.1873674E-03 4.2728424E-02 at 100iterations 5.5585819E-04 1.9517899E-02 at 110iterations 2.8696490E-04 1.0653973E-02 at 120iterations finished qdiffx linear iterations at : 11:37:34 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 2.8696490E-04 1.0653973E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 11:37:35 9.038u 0.304s 0:10.14 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 Sat Oct 8 2011 at 11:37:35 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 = 4086 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.316703 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 2.316703 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.985960 assigned positive charge : 614.0102 centred at (gu) : 84.14024 88.80602 92.50266 assigned negative charge : -621.9982 centred at (gu) : 84.36795 89.08201 92.70094 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 178642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31427 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 80278 mr = 133565 m= 20318 mr = 63894 m= 2968 mr = 15063 m= 123 mr = 1813 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2468 time to turn everything in is 0.9500000 number of dielectric boundary points 67972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 31384 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) : 1.544469 object centre at (A) : 30.99100 14.66550 12.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3728377 -0.2223787 midg,1,midg; midg,igrid,midg -7.7725247E-02 -0.1436366 1,midg,midg; igrid,midg,midg 0.3230397 -0.4257792 gauss-seidel spectral radius is 0.9991160 estimated iterations to convergence 266 setup time was (sec) 1.220000 now iterating at: 11:37:36 rms-change max change #iterations 9.402350 372.1942 at 10iterations 5.238636 137.2286 at 20iterations 2.909605 66.11507 at 30iterations 1.609612 31.04969 at 40iterations 0.8874854 18.11045 at 50iterations 0.4881597 9.168137 at 60iterations 0.2674707 5.366244 at 70iterations 0.1466197 2.835231 at 80iterations 8.0319539E-02 1.672356 at 90iterations 4.4021267E-02 0.9097290 at 100iterations 2.4128266E-02 0.4522629 at 110iterations 1.3234488E-02 0.2850952 at 120iterations 7.2714919E-03 0.1495762 at 130iterations 4.0163356E-03 7.8155518E-02 at 140iterations 2.2443384E-03 4.3138504E-02 at 150iterations 1.2727488E-03 2.6466370E-02 at 160iterations 7.4316491E-04 1.5161514E-02 at 170iterations 4.5154648E-04 9.5715523E-03 at 180iterations finished qdiffx linear iterations at : 11:37:50 total time elapsed so far: 14.51000 # loops : 180 mean,max change (kT/e) : 4.5154648E-04 9.5715523E-03 energy calculations done at 14.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.65000 DelPhi exited at 11:37:50 14.648u 0.313s 0:15.31 97.6% 0+0k 0+0io 0pf+0w