Mon Oct 10 17:03:40 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 Mon Oct 10 2011 at 17:03:40 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 = 4854 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5117958 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 0.5117958 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4607 net assigned charge : 7.800048 assigned positive charge : 730.1041 centred at (gu) : 90.34562 90.27813 88.48899 assigned negative charge : -722.3088 centred at (gu) : 90.21922 90.30371 88.46352 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8040 nv = 96 ne = 84 npr = 97917 no. pairs analyzed = 97917 no. exposed pairs = 6132 no. arc points = 42374 no. surface atoms = 2068 nbur = 2786 mkacc time = 0.2300000 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= 285 mr = 4134 m= 0 mr = 7 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4110 ## 592 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10672 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6470426E-11 1.2647210E-10 midg,1,midg; midg,igrid,midg 1.7390857E-10 4.9164946E-11 1,midg,midg; igrid,midg,midg -2.1597754E-10 5.0292381E-10 gauss-seidel spectral radius is 0.9804815 estimated iterations to convergence 59 setup time was (sec) 0.7600000 now iterating at: 17:03:42 rms-change max change #iterations 6.8862684E-02 9.019140 at 10iterations 4.6223206E-03 0.7006683 at 20iterations 7.7035587E-04 9.6015930E-02 at 30iterations 2.6657415E-04 3.3317327E-02 at 40iterations 1.0387733E-04 1.4941573E-02 at 50iterations finished qdiffx linear iterations at : 17:03:44 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.0387733E-04 1.4941573E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:03:46 3.599u 0.167s 0:05.55 67.5% 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 Mon Oct 10 2011 at 17:03:46 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 = 4854 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.535387 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 1.535387 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4607 net assigned charge : 7.800048 assigned positive charge : 730.1041 centred at (gu) : 91.03537 90.83314 85.46537 assigned negative charge : -722.3088 centred at (gu) : 90.65730 90.91088 85.39009 start vw surface at 0.2500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 91037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25876 mr = 62467 m= 2172 mr = 16734 m= 60 mr = 897 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 39046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 34621 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) : 0.5117958 object centre at (A) : 9.010001 2.354501 30.73950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2242332E-03 1.9315284E-02 midg,1,midg; midg,igrid,midg 2.0271849E-03 -1.0319726E-02 1,midg,midg; igrid,midg,midg -5.8655825E-04 1.4549973E-02 gauss-seidel spectral radius is 0.9981315 estimated iterations to convergence 184 setup time was (sec) 1.030000 now iterating at: 17:03:47 rms-change max change #iterations 3.830059 141.3197 at 10iterations 1.571796 51.61867 at 20iterations 0.6490877 20.15161 at 30iterations 0.2684425 8.839619 at 40iterations 0.1105695 3.532284 at 50iterations 4.5545682E-02 1.461842 at 60iterations 1.8805709E-02 0.6065178 at 70iterations 7.8420285E-03 0.2638016 at 80iterations 3.2956812E-03 9.9372864E-02 at 90iterations 1.4141074E-03 4.4517517E-02 at 100iterations 6.4627366E-04 2.1234512E-02 at 110iterations 3.2976907E-04 1.0396004E-02 at 120iterations finished qdiffx linear iterations at : 17:03:54 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 3.2976907E-04 1.0396004E-02 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 17:03:56 8.465u 0.224s 0:09.59 90.5% 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 Mon Oct 10 2011 at 17:03:56 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 = 4854 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.303081 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 2.303081 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4607 net assigned charge : 7.800048 assigned positive charge : 730.1041 centred at (gu) : 91.55270 91.24924 83.19772 assigned negative charge : -722.3088 centred at (gu) : 90.98592 91.36626 83.08498 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 212480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93440 mr = 153599 m= 22944 mr = 72378 m= 3146 mr = 16017 m= 179 mr = 1815 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 88324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 36751 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) : 1.535387 object centre at (A) : 9.010001 2.354501 30.73950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1235886 0.4798654 midg,1,midg; midg,igrid,midg -9.0774834E-02 -0.2838157 1,midg,midg; igrid,midg,midg 3.8888946E-03 0.2194427 gauss-seidel spectral radius is 0.9991711 estimated iterations to convergence 274 setup time was (sec) 2.080000 now iterating at: 17:03:58 rms-change max change #iterations 10.44427 274.0717 at 10iterations 6.031792 140.8468 at 20iterations 3.446926 82.49895 at 30iterations 1.958557 44.64831 at 40iterations 1.109791 23.82680 at 50iterations 0.6273081 14.42174 at 60iterations 0.3523907 6.992153 at 70iterations 0.1980162 3.854767 at 80iterations 0.1108947 2.466753 at 90iterations 6.2138587E-02 1.299736 at 100iterations 3.4723941E-02 0.6885038 at 110iterations 1.9397072E-02 0.3596239 at 120iterations 1.0847689E-02 0.2078037 at 130iterations 6.0639740E-03 0.1070004 at 140iterations 3.3806125E-03 6.7850113E-02 at 150iterations 1.8912867E-03 3.5011292E-02 at 160iterations 1.0593078E-03 2.0359039E-02 at 170iterations 5.9679186E-04 1.1646271E-02 at 180iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 5.9679186E-04 1.1646271E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.55000 DelPhi exited at 17:04:13 15.555u 0.282s 0:17.05 92.8% 0+0k 0+0io 0pf+0w