Sat Oct 15 14:46:53 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 Sat Oct 15 2011 at 14:46:53 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5697276 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 0.5697276 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.485974 assigned positive charge : 413.6583 centred at (gu) : 89.95427 89.81689 89.03088 assigned negative charge : -415.1454 centred at (gu) : 89.98827 89.65141 88.85815 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5863 nv = 96 ne = 84 npr = 54117 no. pairs analyzed = 54117 no. exposed pairs = 3655 no. arc points = 26121 no. surface atoms = 1228 nbur = 1510 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= 229 mr = 2917 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2642 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4818588E-09 1.7942212E-09 midg,1,midg; midg,igrid,midg -2.7608398E-09 2.0725897E-09 1,midg,midg; igrid,midg,midg 3.0627420E-10 -6.7734524E-10 gauss-seidel spectral radius is 0.9840890 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 14:46:54 rms-change max change #iterations 8.6055659E-02 12.64642 at 10iterations 6.4322809E-03 1.077667 at 20iterations 4.8169418E-04 7.3049545E-02 at 30iterations 3.5569297E-05 6.6108704E-03 at 40iterations 2.7705757E-06 4.6539307E-04 at 50iterations finished qdiffx linear iterations at : 14:46:58 total time elapsed so far: 5.380000 # loops : 50 mean,max change (kT/e) : 2.7705757E-06 4.6539307E-04 energy calculations done at 5.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.560000 DelPhi exited at 14:46:59 5.562u 0.440s 0:06.31 95.0% 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 Sat Oct 15 2011 at 14:46:59 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.709183 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 1.709183 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.485974 assigned positive charge : 413.6583 centred at (gu) : 89.86205 89.45013 87.09212 assigned negative charge : -415.1454 centred at (gu) : 89.96446 88.95410 86.57414 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26121 grid for indexing accessible points = 1.400000 m= 19337 mr = 42630 m= 2008 mr = 13054 m= 55 mr = 944 m= 0 mr = 9 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 469 time to turn everything in is 0.5200000 number of dielectric boundary points 29363 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 0.6800000 number of grid points assigned charge 20127 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) : 0.5697276 object centre at (A) : 17.59400 -4.682000 -18.03150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1257656E-02 5.4113497E-03 midg,1,midg; midg,igrid,midg -6.2278048E-03 5.1104338E-03 1,midg,midg; igrid,midg,midg 1.0834814E-02 9.0347056E-04 gauss-seidel spectral radius is 0.9983280 estimated iterations to convergence 194 setup time was (sec) 0.9000000 now iterating at: 14:47:00 rms-change max change #iterations 3.529057 167.3397 at 10iterations 1.527219 59.52477 at 20iterations 0.6589498 23.78494 at 30iterations 0.2853560 10.67301 at 40iterations 0.1233888 4.834843 at 50iterations 5.3170167E-02 2.050592 at 60iterations 2.2921156E-02 0.8265533 at 70iterations 9.9260211E-03 0.3792067 at 80iterations 4.2958725E-03 0.1537857 at 90iterations 1.8523923E-03 7.8186035E-02 at 100iterations 8.0324395E-04 2.8697968E-02 at 110iterations 3.4564696E-04 1.1985779E-02 at 120iterations finished qdiffx linear iterations at : 14:47:13 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 3.4564696E-04 1.1985779E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:47:13 13.393u 0.503s 0:14.35 96.7% 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 Sat Oct 15 2011 at 14:47:13 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.563774 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): -13.64900 48.83700 ymin,ymax (A): -27.22000 17.85600 zmin,zma (A): -41.71800 5.655000 x,y,z range (A): 62.48600 45.07600 47.37300 scale (grids/A): 2.563774 object centre (A): 17.59400 -4.682000 -18.03150 number of atom coordinates read : 2738 total number of charged atoms : 2599 net assigned charge : -1.485974 assigned positive charge : 413.6583 centred at (gu) : 89.79276 89.17480 85.63804 assigned negative charge : -415.1454 centred at (gu) : 89.94660 88.43095 84.86118 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 150015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26121 grid for indexing accessible points = 1.400000 m= 67313 mr = 104779 m= 18784 mr = 52405 m= 2985 mr = 13800 m= 178 mr = 1880 m= 3 mr = 95 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1502 time to turn everything in is 1.340000 number of dielectric boundary points 66317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 20783 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) : 1.709183 object centre at (A) : 17.59400 -4.682000 -18.03150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2627406 9.2243470E-02 midg,1,midg; midg,igrid,midg -6.5291338E-02 5.4357596E-02 1,midg,midg; igrid,midg,midg 0.1830452 0.3611129 gauss-seidel spectral radius is 0.9991855 estimated iterations to convergence 277 setup time was (sec) 1.730000 now iterating at: 14:47:16 rms-change max change #iterations 9.023667 339.2814 at 10iterations 5.171421 140.1492 at 20iterations 2.952979 78.34447 at 30iterations 1.670511 40.00634 at 40iterations 0.9441530 21.88889 at 50iterations 0.5310550 11.20584 at 60iterations 0.2986090 6.292402 at 70iterations 0.1675619 3.480037 at 80iterations 9.3761101E-02 2.094393 at 90iterations 5.2686192E-02 1.068161 at 100iterations 2.9467074E-02 0.5771542 at 110iterations 1.6465031E-02 0.3449898 at 120iterations 9.2193149E-03 0.1823177 at 130iterations 5.1526246E-03 0.1077254 at 140iterations 2.8770699E-03 5.7041883E-02 at 150iterations 1.6096758E-03 3.4107208E-02 at 160iterations 8.9772063E-04 1.7574310E-02 at 170iterations 5.0177227E-04 1.0424614E-02 at 180iterations finished qdiffx linear iterations at : 14:47:37 total time elapsed so far: 23.10000 # loops : 180 mean,max change (kT/e) : 5.0177227E-04 1.0424614E-02 energy calculations done at 23.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.27000 DelPhi exited at 14:47:38 23.276u 0.527s 0:24.16 98.4% 0+0k 0+0io 0pf+0w