Tue Oct 11 08:22:15 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 Tue Oct 11 2011 at 08:22:15 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 = 3163 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: 0.5770135 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): -15.32000 38.87400 ymin,ymax (A): 5.385000 67.08200 zmin,zma (A): 91.39200 150.2240 x,y,z range (A): 54.19400 61.69700 58.83200 scale (grids/A): 0.5770135 object centre (A): 11.77700 36.23350 120.8080 number of atom coordinates read : 3163 total number of charged atoms : 3024 net assigned charge : -5.999976 assigned positive charge : 471.1039 centred at (gu) : 90.63274 89.85018 92.02399 assigned negative charge : -477.1049 centred at (gu) : 90.59816 89.87980 92.01434 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6832 nv = 96 ne = 84 npr = 65275 no. pairs analyzed = 65275 no. exposed pairs = 3930 no. arc points = 27392 no. surface atoms = 1329 nbur = 1834 mkacc time = 0.1800000 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= 309 mr = 3659 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2784 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7928220E-10 -1.5563517E-09 midg,1,midg; midg,igrid,midg -5.7617411E-10 -1.7566356E-09 1,midg,midg; igrid,midg,midg -1.6629546E-09 -5.1722054E-10 gauss-seidel spectral radius is 0.9845118 estimated iterations to convergence 66 setup time was (sec) 0.6800000 now iterating at: 08:22:16 rms-change max change #iterations 0.1013236 15.22975 at 10iterations 7.8582298E-03 1.194126 at 20iterations 6.7823863E-04 0.1185045 at 30iterations 9.4993513E-05 1.7097950E-02 at 40iterations 2.4548037E-05 4.9738884E-03 at 50iterations finished qdiffx linear iterations at : 08:22:19 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 2.4548037E-05 4.9738884E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 08:22:20 4.245u 0.291s 0:04.83 93.7% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 08:22:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 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: 1.731040 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): -15.32000 38.87400 ymin,ymax (A): 5.385000 67.08200 zmin,zma (A): 91.39200 150.2240 x,y,z range (A): 54.19400 61.69700 58.83200 scale (grids/A): 1.731040 object centre (A): 11.77700 36.23350 120.8080 number of atom coordinates read : 3163 total number of charged atoms : 3024 net assigned charge : -5.999976 assigned positive charge : 471.1039 centred at (gu) : 91.89716 89.54968 96.07136 assigned negative charge : -477.1049 centred at (gu) : 91.79429 89.63927 96.04264 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27392 grid for indexing accessible points = 1.400000 m= 24948 mr = 50900 m= 3236 mr = 17722 m= 107 mr = 1777 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1289 time to turn everything in is 0.6800000 number of dielectric boundary points 32250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 23473 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) : 0.5770135 object centre at (A) : 11.77700 36.23350 120.8080 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8274683E-03 7.0328005E-03 midg,1,midg; midg,igrid,midg -2.1521010E-02 -2.9589564E-02 1,midg,midg; igrid,midg,midg -5.8918120E-03 3.6810120E-03 gauss-seidel spectral radius is 0.9984037 estimated iterations to convergence 199 setup time was (sec) 0.9800000 now iterating at: 08:22:21 rms-change max change #iterations 3.875867 164.5328 at 10iterations 1.702338 66.26550 at 20iterations 0.7463788 26.09759 at 30iterations 0.3300963 11.39267 at 40iterations 0.1452039 4.906327 at 50iterations 6.3958660E-02 2.180506 at 60iterations 2.8159617E-02 0.9067688 at 70iterations 1.2402225E-02 0.4182889 at 80iterations 5.4966654E-03 0.1892395 at 90iterations 2.4309335E-03 7.9784393E-02 at 100iterations 1.0881681E-03 3.4644395E-02 at 110iterations 4.9574370E-04 1.4759064E-02 at 120iterations finished qdiffx linear iterations at : 08:22:30 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 4.9574370E-04 1.4759064E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 08:22:30 9.736u 0.334s 0:10.34 97.2% 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 Tue Oct 11 2011 at 08:22:30 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 = 3163 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: 2.596561 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): -15.32000 38.87400 ymin,ymax (A): 5.385000 67.08200 zmin,zma (A): 91.39200 150.2240 x,y,z range (A): 54.19400 61.69700 58.83200 scale (grids/A): 2.596561 object centre (A): 11.77700 36.23350 120.8080 number of atom coordinates read : 3163 total number of charged atoms : 3024 net assigned charge : -5.999976 assigned positive charge : 471.1039 centred at (gu) : 92.84565 89.32432 99.10692 assigned negative charge : -477.1049 centred at (gu) : 92.69125 89.45876 99.06396 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27392 grid for indexing accessible points = 1.400000 m= 83028 mr = 123754 m= 27331 mr = 66570 m= 5302 mr = 21248 m= 502 mr = 3760 m= 21 mr = 270 m= 0 mr = 13 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 4668 time to turn everything in is 1.690000 number of dielectric boundary points 72879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 24169 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) : 1.731040 object centre at (A) : 11.77700 36.23350 120.8080 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6816070E-02 9.1455288E-02 midg,1,midg; midg,igrid,midg -0.1533130 -0.2782874 1,midg,midg; igrid,midg,midg 1.0583819E-02 2.8747624E-02 gauss-seidel spectral radius is 0.9992071 estimated iterations to convergence 280 setup time was (sec) 2.030000 now iterating at: 08:22:33 rms-change max change #iterations 9.635126 315.9530 at 10iterations 5.544265 146.6539 at 20iterations 3.158343 66.33868 at 30iterations 1.801384 38.18381 at 40iterations 1.022873 22.91984 at 50iterations 0.5792112 11.08797 at 60iterations 0.3277870 5.886879 at 70iterations 0.1853963 4.018909 at 80iterations 0.1046688 2.036220 at 90iterations 5.9019774E-02 1.186451 at 100iterations 3.3330575E-02 0.6207790 at 110iterations 1.8821353E-02 0.3352928 at 120iterations 1.0617421E-02 0.2027411 at 130iterations 5.9958822E-03 0.1161098 at 140iterations 3.3917238E-03 7.0232391E-02 at 150iterations 1.9166382E-03 3.6018372E-02 at 160iterations 1.0940387E-03 2.1083832E-02 at 170iterations 6.2971038E-04 1.2870550E-02 at 180iterations finished qdiffx linear iterations at : 08:22:47 total time elapsed so far: 16.39000 # loops : 180 mean,max change (kT/e) : 6.2971038E-04 1.2870550E-02 energy calculations done at 16.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.57000 DelPhi exited at 08:22:48 16.569u 0.358s 0:17.89 94.5% 0+0k 0+0io 0pf+0w