Tue Oct 11 06:56:37 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+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 Tue Oct 11 2011 at 06:56:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5623657 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 0.5623657 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : 5.3013653E-02 assigned positive charge : 434.4395 centred at (gu) : 90.22335 90.13241 89.41557 assigned negative charge : -434.3873 centred at (gu) : 90.20663 90.25123 89.41592 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6189 nv = 96 ne = 84 npr = 60842 no. pairs analyzed = 60842 no. exposed pairs = 3771 no. arc points = 27077 no. surface atoms = 1285 nbur = 1681 mkacc time = 0.2000000 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 = 1.540000 m= 258 mr = 3211 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4300000 number of dielectric boundary points 3217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2720 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4741826E-11 3.8019492E-12 midg,1,midg; midg,igrid,midg 1.3435844E-09 -1.4581244E-09 1,midg,midg; igrid,midg,midg -1.7862624E-10 2.1659803E-10 gauss-seidel spectral radius is 0.9836921 estimated iterations to convergence 64 setup time was (sec) 0.7800000 now iterating at: 06:56:38 rms-change max change #iterations 8.4853232E-02 13.45067 at 10iterations 6.0616178E-03 0.9817367 at 20iterations 4.6686950E-04 6.7493439E-02 at 30iterations 4.0761766E-05 6.8359375E-03 at 40iterations 5.0704025E-06 1.0232925E-03 at 50iterations finished qdiffx linear iterations at : 06:56:42 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 5.0704025E-06 1.0232925E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 06:56:43 4.802u 0.441s 0:05.59 93.7% 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 06:56:43 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.687097 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 1.687097 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : 5.3013653E-02 assigned positive charge : 434.4395 centred at (gu) : 90.66956 90.39674 88.24616 assigned negative charge : -434.3873 centred at (gu) : 90.61959 90.75341 88.24736 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27077 grid for indexing accessible points = 1.400000 m= 23109 mr = 44847 m= 2871 mr = 16673 m= 76 mr = 1600 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 544 time to turn everything in is 0.7100000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 21808 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) : 0.5623657 object centre at (A) : 10.88300 49.15850 -46.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5676717E-03 1.3091699E-02 midg,1,midg; midg,igrid,midg -1.9964667E-03 -2.7624934E-04 1,midg,midg; igrid,midg,midg 3.9642639E-03 -8.5254889E-03 gauss-seidel spectral radius is 0.9983113 estimated iterations to convergence 193 setup time was (sec) 1.050000 now iterating at: 06:56:44 rms-change max change #iterations 3.511072 195.3577 at 10iterations 1.503707 56.26492 at 20iterations 0.6473280 22.87857 at 30iterations 0.2788769 10.58467 at 40iterations 0.1199302 4.206212 at 50iterations 5.1585682E-02 1.895523 at 60iterations 2.2082848E-02 0.7347851 at 70iterations 9.5427018E-03 0.3250991 at 80iterations 4.1148528E-03 0.1421967 at 90iterations 1.7700568E-03 5.8734894E-02 at 100iterations 7.6579524E-04 2.7890205E-02 at 110iterations 3.3051148E-04 1.1505127E-02 at 120iterations finished qdiffx linear iterations at : 06:56:54 total time elapsed so far: 10.77000 # loops : 120 mean,max change (kT/e) : 3.3051148E-04 1.1505127E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 06:56:54 10.993u 0.480s 0:11.76 97.5% 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 Tue Oct 11 2011 at 06:56:55 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.530646 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): -20.76900 42.53500 ymin,ymax (A): 21.37900 76.93800 zmin,zma (A): -72.73800 -21.17100 x,y,z range (A): 63.30400 55.55901 51.56700 scale (grids/A): 2.530646 object centre (A): 10.88300 49.15850 -46.95450 number of atom coordinates read : 2966 total number of charged atoms : 2825 net assigned charge : 5.3013653E-02 assigned positive charge : 434.4395 centred at (gu) : 91.00416 90.59503 87.36912 assigned negative charge : -434.3873 centred at (gu) : 90.92937 91.13010 87.37090 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 154941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27077 grid for indexing accessible points = 1.400000 m= 75749 mr = 109299 m= 25473 mr = 60841 m= 4730 mr = 20177 m= 317 mr = 3392 m= 1 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1835 time to turn everything in is 1.750000 number of dielectric boundary points 67364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 22583 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) : 1.687097 object centre at (A) : 10.88300 49.15850 -46.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4397741E-02 0.2320050 midg,1,midg; midg,igrid,midg -4.2768978E-03 1.2140944E-02 1,midg,midg; igrid,midg,midg -2.4477698E-02 -0.1734217 gauss-seidel spectral radius is 0.9991794 estimated iterations to convergence 276 setup time was (sec) 2.120000 now iterating at: 06:56:57 rms-change max change #iterations 8.954878 280.7823 at 10iterations 5.105455 146.7314 at 20iterations 2.900693 80.85155 at 30iterations 1.634055 39.55046 at 40iterations 0.9203075 19.21363 at 50iterations 0.5160445 11.28244 at 60iterations 0.2898889 6.370678 at 70iterations 0.1622298 3.550240 at 80iterations 9.0656795E-02 1.846447 at 90iterations 5.0666757E-02 1.026932 at 100iterations 2.8215325E-02 0.5902843 at 110iterations 1.5767630E-02 0.3467045 at 120iterations 8.8115241E-03 0.1656456 at 130iterations 4.9178912E-03 0.1010056 at 140iterations 2.7340166E-03 5.4099083E-02 at 150iterations 1.5249555E-03 3.2764435E-02 at 160iterations 8.5120409E-04 1.5713215E-02 at 170iterations 4.7494072E-04 9.2267990E-03 at 180iterations finished qdiffx linear iterations at : 06:57:13 total time elapsed so far: 18.07000 # loops : 180 mean,max change (kT/e) : 4.7494072E-04 9.2267990E-03 energy calculations done at 18.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.30000 DelPhi exited at 06:57:14 18.300u 0.507s 0:19.38 97.0% 0+0k 0+0io 0pf+0w