Sat Oct 8 11:38:37 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 Sat Oct 8 2011 at 11:38:38 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 = 3514 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4975889 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 0.4975889 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.999975 assigned positive charge : 520.1529 centred at (gu) : 89.91001 90.70963 91.63922 assigned negative charge : -524.1547 centred at (gu) : 89.81711 90.73404 91.67425 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5667 nv = 96 ne = 84 npr = 66798 no. pairs analyzed = 66798 no. exposed pairs = 5231 no. arc points = 38191 no. surface atoms = 1749 nbur = 1765 mkacc time = 0.1200000 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 = 1.708000 m= 187 mr = 2379 m= 0 mr = 1 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3670 ## 602 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2511285E-12 -1.0586821E-10 midg,1,midg; midg,igrid,midg -3.5552533E-12 -6.8230588E-11 1,midg,midg; igrid,midg,midg -1.3421204E-10 6.6479780E-11 gauss-seidel spectral radius is 0.9792843 estimated iterations to convergence 58 setup time was (sec) 0.4300000 now iterating at: 11:38:38 rms-change max change #iterations 4.7828168E-02 9.213158 at 10iterations 2.3877765E-03 0.4226322 at 20iterations 1.5859761E-04 3.3653259E-02 at 30iterations 2.3675948E-05 5.3586960E-03 at 40iterations 5.1232159E-06 1.1835098E-03 at 50iterations finished qdiffx linear iterations at : 11:38:41 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.1232159E-06 1.1835098E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 11:38:41 3.479u 0.189s 0:03.96 92.1% 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 Sat Oct 8 2011 at 11:38:42 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 = 3514 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.492767 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 1.492767 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.999975 assigned positive charge : 520.1529 centred at (gu) : 89.72909 92.12772 94.91682 assigned negative charge : -524.1547 centred at (gu) : 89.45065 92.20184 95.02247 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15423 mr = 37876 m= 1082 mr = 8971 m= 17 mr = 292 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 0.3200000 number of dielectric boundary points 32393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 526 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 24983 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) : 0.4975889 object centre at (A) : 6.299001 5.564499 18.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0989791E-05 -4.4609183E-03 midg,1,midg; midg,igrid,midg -9.2525249E-03 -3.7961712E-03 1,midg,midg; igrid,midg,midg -3.1629696E-03 1.6007123E-04 gauss-seidel spectral radius is 0.9978953 estimated iterations to convergence 173 setup time was (sec) 0.5200000 now iterating at: 11:38:42 rms-change max change #iterations 2.929796 147.3163 at 10iterations 1.138901 47.19420 at 20iterations 0.4395425 17.31422 at 30iterations 0.1706395 6.438816 at 40iterations 6.6234544E-02 2.550507 at 50iterations 2.5753127E-02 1.066128 at 60iterations 9.9965855E-03 0.3641758 at 70iterations 3.9001945E-03 0.1549273 at 80iterations 1.5147836E-03 5.4605484E-02 at 90iterations 5.9594167E-04 2.3299217E-02 at 100iterations 2.3394803E-04 8.7356567E-03 at 110iterations 9.3123330E-05 3.7412643E-03 at 120iterations finished qdiffx linear iterations at : 11:38:56 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 9.3123330E-05 3.7412643E-03 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 11:38:57 7.737u 0.222s 0:15.01 52.9% 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 Sat Oct 8 2011 at 11:38:57 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 = 3514 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.239150 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 2.239150 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.999975 assigned positive charge : 520.1529 centred at (gu) : 89.59346 93.19138 97.37492 assigned negative charge : -524.1547 centred at (gu) : 89.17594 93.30254 97.53363 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 56786 mr = 94700 m= 12339 mr = 40436 m= 1305 mr = 7992 m= 46 mr = 622 m= 0 mr = 3 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 73272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 26710 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) : 1.492767 object centre at (A) : 6.299001 5.564499 18.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3567568E-02 2.0964084E-02 midg,1,midg; midg,igrid,midg -0.2375551 -6.3628428E-02 1,midg,midg; igrid,midg,midg -4.9281377E-02 6.5818736E-03 gauss-seidel spectral radius is 0.9990705 estimated iterations to convergence 259 setup time was (sec) 0.9900000 now iterating at: 11:38:58 rms-change max change #iterations 8.214787 235.0531 at 10iterations 4.590415 124.2002 at 20iterations 2.542726 65.15343 at 30iterations 1.395823 36.85984 at 40iterations 0.7634814 20.05440 at 50iterations 0.4163546 11.57941 at 60iterations 0.2260367 5.482210 at 70iterations 0.1226504 3.100295 at 80iterations 6.6282012E-02 1.492834 at 90iterations 3.5802860E-02 0.8235044 at 100iterations 1.9348389E-02 0.4652915 at 110iterations 1.0395722E-02 0.2319036 at 120iterations 5.6132469E-03 0.1458058 at 130iterations 3.0110679E-03 6.6339493E-02 at 140iterations 1.6228104E-03 3.7841797E-02 at 150iterations 8.7289425E-04 1.7956972E-02 at 160iterations 4.6909996E-04 1.0671616E-02 at 170iterations 2.5212934E-04 5.2528381E-03 at 180iterations finished qdiffx linear iterations at : 11:39:10 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 2.5212934E-04 5.2528381E-03 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 11:39:11 13.316u 0.235s 0:13.96 96.9% 0+0k 0+0io 0pf+0w