Sun Oct 9 17:04:57 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 Sun Oct 9 2011 at 17:04:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 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: 0.5228374 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): -23.21900 44.87100 ymin,ymax (A): -44.42200 22.33200 zmin,zma (A): 8.346001 68.86600 x,y,z range (A): 68.09000 66.75400 60.52000 scale (grids/A): 0.5228374 object centre (A): 10.82600 -11.04500 38.60600 number of atom coordinates read : 5325 total number of charged atoms : 5164 net assigned charge : 7.000046 assigned positive charge : 805.0085 centred at (gu) : 90.35473 90.08009 90.16256 assigned negative charge : -798.0146 centred at (gu) : 90.30870 89.93503 90.31521 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9474 nv = 96 ne = 84 npr = 104163 no. pairs analyzed = 104163 no. exposed pairs = 7039 no. arc points = 50002 no. surface atoms = 2334 nbur = 2991 mkacc time = 0.2400000 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= 346 mr = 4764 m= 0 mr = 14 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5200000 number of dielectric boundary points 5042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4965 ## 709 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5717577E-10 -6.0845085E-10 midg,1,midg; midg,igrid,midg -5.3309335E-10 8.7684837E-10 1,midg,midg; igrid,midg,midg -4.8098404E-11 4.2915380E-10 gauss-seidel spectral radius is 0.9813409 estimated iterations to convergence 60 setup time was (sec) 0.7400000 now iterating at: 17:04:58 rms-change max change #iterations 8.4665887E-02 10.91368 at 10iterations 8.4097357E-03 1.276421 at 20iterations 1.9071354E-03 0.2887115 at 30iterations 5.5474689E-04 7.6362610E-02 at 40iterations 1.7254474E-04 2.1881104E-02 at 50iterations finished qdiffx linear iterations at : 17:05:00 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.7254474E-04 2.1881104E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:05:01 3.545u 0.156s 0:03.98 92.7% 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 Sun Oct 9 2011 at 17:05:01 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 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: 1.568512 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): -23.21900 44.87100 ymin,ymax (A): -44.42200 22.33200 zmin,zma (A): 8.346001 68.86600 x,y,z range (A): 68.09000 66.75400 60.52000 scale (grids/A): 1.568512 object centre (A): 10.82600 -11.04500 38.60600 number of atom coordinates read : 5325 total number of charged atoms : 5164 net assigned charge : 7.000046 assigned positive charge : 805.0085 centred at (gu) : 91.06267 90.23825 90.48638 assigned negative charge : -798.0146 centred at (gu) : 90.92573 89.80499 90.94533 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 105594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31165 mr = 70917 m= 3050 mr = 20560 m= 74 mr = 1416 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 671 time to turn everything in is 0.7500000 number of dielectric boundary points 46990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 685 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 39091 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) : 0.5228374 object centre at (A) : 10.82600 -11.04500 38.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3112075E-02 1.8827002E-03 midg,1,midg; midg,igrid,midg -7.9275453E-03 3.4633003E-02 1,midg,midg; igrid,midg,midg -1.8852441E-02 2.1555942E-02 gauss-seidel spectral radius is 0.9982895 estimated iterations to convergence 192 setup time was (sec) 1.040000 now iterating at: 17:05:02 rms-change max change #iterations 4.311575 175.0470 at 10iterations 1.830600 59.59758 at 20iterations 0.7831460 22.16135 at 30iterations 0.3353092 10.29819 at 40iterations 0.1435277 4.539314 at 50iterations 6.1731644E-02 1.676077 at 60iterations 2.6802307E-02 0.9239483 at 70iterations 1.1755016E-02 0.3374729 at 80iterations 5.2499296E-03 0.1548157 at 90iterations 2.4596502E-03 7.2795868E-02 at 100iterations 1.2259452E-03 3.4835815E-02 at 110iterations 6.5936759E-04 1.8626213E-02 at 120iterations finished qdiffx linear iterations at : 17:05:08 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 6.5936759E-04 1.8626213E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 17:05:09 7.736u 0.172s 0:08.22 96.1% 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 Sun Oct 9 2011 at 17:05:09 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 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: 2.352768 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): -23.21900 44.87100 ymin,ymax (A): -44.42200 22.33200 zmin,zma (A): 8.346001 68.86600 x,y,z range (A): 68.09000 66.75400 60.52000 scale (grids/A): 2.352768 object centre (A): 10.82600 -11.04500 38.60600 number of atom coordinates read : 5325 total number of charged atoms : 5164 net assigned charge : 7.000046 assigned positive charge : 805.0085 centred at (gu) : 91.59349 90.35674 90.72914 assigned negative charge : -798.0146 centred at (gu) : 91.38860 89.70739 91.41788 start vw surface at 0.2300000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 245880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 110148 mr = 174949 m= 29445 mr = 85006 m= 4535 mr = 21367 m= 278 mr = 2859 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 2285 time to turn everything in is 1.840000 number of dielectric boundary points 106014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 41237 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) : 1.568512 object centre at (A) : 10.82600 -11.04500 38.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5346578 0.1067682 midg,1,midg; midg,igrid,midg -0.1391188 0.6093507 1,midg,midg; igrid,midg,midg -0.4288481 0.4464397 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 2.160000 now iterating at: 17:05:11 rms-change max change #iterations 11.58255 303.6665 at 10iterations 6.867794 176.5326 at 20iterations 4.050574 86.36436 at 30iterations 2.375705 52.53982 at 40iterations 1.382103 32.53278 at 50iterations 0.8022447 17.85993 at 60iterations 0.4645424 9.060715 at 70iterations 0.2683952 4.977646 at 80iterations 0.1545203 2.901475 at 90iterations 8.9018084E-02 1.675567 at 100iterations 5.1133547E-02 0.8732165 at 110iterations 2.9334119E-02 0.5018493 at 120iterations 1.6863631E-02 0.3119035 at 130iterations 9.6641593E-03 0.1693344 at 140iterations 5.5605983E-03 9.6954346E-02 at 150iterations 3.1955261E-03 6.0663223E-02 at 160iterations 1.8449326E-03 3.6012650E-02 at 170iterations 1.0699742E-03 1.8478394E-02 at 180iterations finished qdiffx linear iterations at : 17:05:22 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.0699742E-03 1.8478394E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 17:05:23 13.249u 0.179s 0:13.71 97.8% 0+0k 0+0io 0pf+0w