Mon Oct 10 17:04:18 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 17:04:19 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 = 2684 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: 0.5723749 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 0.5723749 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4999765 assigned positive charge : 401.7685 centred at (gu) : 89.24258 89.89657 89.86407 assigned negative charge : -402.2695 centred at (gu) : 89.28512 89.77773 89.77290 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5794 nv = 96 ne = 84 npr = 53412 no. pairs analyzed = 53412 no. exposed pairs = 3729 no. arc points = 26297 no. surface atoms = 1251 nbur = 1433 mkacc time = 0.1400000 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 = 1.512000 m= 247 mr = 2786 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2714 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5547762E-09 1.2656386E-09 midg,1,midg; midg,igrid,midg -1.9913942E-09 1.6814182E-09 1,midg,midg; igrid,midg,midg 6.8566330E-10 -6.1949673E-10 gauss-seidel spectral radius is 0.9842315 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 17:04:20 rms-change max change #iterations 8.3763190E-02 14.11050 at 10iterations 6.3751228E-03 1.101331 at 20iterations 4.7222050E-04 0.1011057 at 30iterations 3.5716512E-05 6.2704086E-03 at 40iterations 2.7093556E-06 4.2963028E-04 at 50iterations finished qdiffx linear iterations at : 17:04:23 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 2.7093556E-06 4.2963028E-04 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 17:04:25 4.491u 0.408s 0:06.03 81.0% 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 Mon Oct 10 2011 at 17:04:25 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 = 2684 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: 1.717125 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 1.717125 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4999765 assigned positive charge : 401.7685 centred at (gu) : 87.72691 89.68903 89.59155 assigned negative charge : -402.2695 centred at (gu) : 87.85521 89.33318 89.31828 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26297 grid for indexing accessible points = 1.400000 m= 18864 mr = 40895 m= 2094 mr = 12276 m= 58 mr = 912 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 30258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19670 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) : 0.5723749 object centre at (A) : 19.78250 -4.615500 -18.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2240980E-02 6.8584126E-03 midg,1,midg; midg,igrid,midg -6.8384567E-03 2.2481657E-03 1,midg,midg; igrid,midg,midg 8.8804541E-03 3.5116863E-03 gauss-seidel spectral radius is 0.9983404 estimated iterations to convergence 195 setup time was (sec) 0.8100000 now iterating at: 17:04:26 rms-change max change #iterations 3.479961 181.2665 at 10iterations 1.489124 62.95026 at 20iterations 0.6446034 23.05776 at 30iterations 0.2784808 10.18370 at 40iterations 0.1202655 3.955410 at 50iterations 5.1872849E-02 1.775936 at 60iterations 2.2500489E-02 0.7932620 at 70iterations 9.6939579E-03 0.3414037 at 80iterations 4.2067762E-03 0.1407042 at 90iterations 1.8190586E-03 6.9396973E-02 at 100iterations 7.8347686E-04 2.9106140E-02 at 110iterations 3.4031144E-04 1.2710094E-02 at 120iterations finished qdiffx linear iterations at : 17:04:35 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 3.4031144E-04 1.2710094E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.30000 DelPhi exited at 17:04:36 10.301u 0.443s 0:11.33 94.7% 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 Mon Oct 10 2011 at 17:04:36 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 = 2684 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: 2.575687 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 2.575687 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4999765 assigned positive charge : 401.7685 centred at (gu) : 86.59024 89.53341 89.38723 assigned negative charge : -402.2695 centred at (gu) : 86.78278 88.99970 88.97739 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26297 grid for indexing accessible points = 1.400000 m= 64952 mr = 100824 m= 18694 mr = 49515 m= 3082 mr = 13388 m= 230 mr = 1887 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 68260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20334 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) : 1.717125 object centre at (A) : 19.78250 -4.615500 -18.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1583370 0.1097280 midg,1,midg; midg,igrid,midg -6.9492422E-02 1.8617794E-02 1,midg,midg; igrid,midg,midg 0.1667301 0.2327158 gauss-seidel spectral radius is 0.9991874 estimated iterations to convergence 277 setup time was (sec) 1.590000 now iterating at: 17:04:38 rms-change max change #iterations 8.897573 332.8115 at 10iterations 5.098836 139.8797 at 20iterations 2.895752 74.33158 at 30iterations 1.637904 40.39101 at 40iterations 0.9238888 22.58275 at 50iterations 0.5195225 11.30532 at 60iterations 0.2919288 6.408178 at 70iterations 0.1632182 3.511881 at 80iterations 9.1364533E-02 1.892389 at 90iterations 5.1075578E-02 1.027193 at 100iterations 2.8584778E-02 0.6210022 at 110iterations 1.5973032E-02 0.3446817 at 120iterations 8.9251027E-03 0.1767292 at 130iterations 4.9874960E-03 0.1046300 at 140iterations 2.7839437E-03 5.7544231E-02 at 150iterations 1.5548669E-03 3.2990456E-02 at 160iterations 8.6594047E-04 1.7971992E-02 at 170iterations 4.8441518E-04 1.0757446E-02 at 180iterations finished qdiffx linear iterations at : 17:04:54 total time elapsed so far: 17.03000 # loops : 180 mean,max change (kT/e) : 4.8441518E-04 1.0757446E-02 energy calculations done at 17.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.20000 DelPhi exited at 17:04:54 17.202u 0.485s 0:18.26 96.8% 0+0k 0+0io 0pf+0w