Mon Oct 10 19:03:19 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 Mon Oct 10 2011 at 19:03:19 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: GLU 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6003778 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 0.6003778 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.014013 assigned positive charge : 380.0891 centred at (gu) : 90.59003 90.33425 90.87407 assigned negative charge : -378.0760 centred at (gu) : 90.58487 90.30073 90.89052 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6108 nv = 96 ne = 84 npr = 51056 no. pairs analyzed = 51056 no. exposed pairs = 3258 no. arc points = 22941 no. surface atoms = 1102 nbur = 1459 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3198 m= 0 mr = 30 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2327 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2037366E-09 3.3238842E-10 midg,1,midg; midg,igrid,midg -3.0864172E-10 2.2360629E-09 1,midg,midg; igrid,midg,midg 6.0510136E-10 1.2061216E-09 gauss-seidel spectral radius is 0.9856425 estimated iterations to convergence 68 setup time was (sec) 0.7000000 now iterating at: 19:03:20 rms-change max change #iterations 0.1041688 22.93730 at 10iterations 8.9433007E-03 1.821909 at 20iterations 7.9377770E-04 0.1175718 at 30iterations 8.5867126E-05 1.3583183E-02 at 40iterations 1.5469797E-05 3.1881332E-03 at 50iterations finished qdiffx linear iterations at : 19:03:24 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 1.5469797E-05 3.1881332E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 19:03:24 4.631u 0.395s 0:05.36 93.6% 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 19:03:24 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: GLU 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.801133 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 1.801133 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.014013 assigned positive charge : 380.0891 centred at (gu) : 91.76959 91.00226 92.62192 assigned negative charge : -378.0760 centred at (gu) : 91.75446 90.90213 92.67151 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22941 grid for indexing accessible points = 1.400000 m= 22511 mr = 45606 m= 3354 mr = 15961 m= 179 mr = 1947 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 29420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18990 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) : 0.6003778 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4263443E-02 -1.9528169E-02 midg,1,midg; midg,igrid,midg -2.2692890E-03 8.9891963E-03 1,midg,midg; igrid,midg,midg 2.6805243E-03 -5.9992047E-03 gauss-seidel spectral radius is 0.9984781 estimated iterations to convergence 203 setup time was (sec) 1.030000 now iterating at: 19:03:26 rms-change max change #iterations 3.734461 166.4999 at 10iterations 1.664291 64.71414 at 20iterations 0.7486106 27.21687 at 30iterations 0.3351828 10.95552 at 40iterations 0.1502276 5.317974 at 50iterations 6.7552596E-02 2.208374 at 60iterations 3.0252269E-02 1.016537 at 70iterations 1.3590292E-02 0.4653854 at 80iterations 6.1188089E-03 0.2068405 at 90iterations 2.7643037E-03 8.8314056E-02 at 100iterations 1.2432927E-03 4.3212891E-02 at 110iterations 5.6999322E-04 1.8835068E-02 at 120iterations finished qdiffx linear iterations at : 19:03:35 total time elapsed so far: 10.33000 # loops : 120 mean,max change (kT/e) : 5.6999322E-04 1.8835068E-02 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 19:03:36 10.552u 0.424s 0:11.81 92.8% 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 19:03:36 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: GLU 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.701700 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 2.701700 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.014013 assigned positive charge : 380.0891 centred at (gu) : 92.65433 91.50337 93.93275 assigned negative charge : -378.0760 centred at (gu) : 92.63167 91.35336 94.00735 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 155347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22941 grid for indexing accessible points = 1.400000 m= 73735 mr = 111357 m= 25421 mr = 58842 m= 5753 mr = 19845 m= 698 mr = 4141 m= 36 mr = 404 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 66399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 19395 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) : 1.801133 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3259284 -0.1551107 midg,1,midg; midg,igrid,midg -0.1048409 4.1901406E-02 1,midg,midg; igrid,midg,midg 1.2608625E-02 -9.6305534E-02 gauss-seidel spectral radius is 0.9992149 estimated iterations to convergence 282 setup time was (sec) 2.120000 now iterating at: 19:03:39 rms-change max change #iterations 9.142749 320.1489 at 10iterations 5.293429 141.4426 at 20iterations 3.020750 76.31519 at 30iterations 1.723262 33.18037 at 40iterations 0.9859142 18.88381 at 50iterations 0.5584353 11.44226 at 60iterations 0.3177368 7.074965 at 70iterations 0.1796889 3.641953 at 80iterations 0.1020238 2.020096 at 90iterations 5.7779837E-02 1.123494 at 100iterations 3.2712035E-02 0.6800117 at 110iterations 1.8571537E-02 0.3674278 at 120iterations 1.0530549E-02 0.2279034 at 130iterations 6.0135392E-03 0.1176138 at 140iterations 3.4491213E-03 7.5494766E-02 at 150iterations 2.0016583E-03 5.3113937E-02 at 160iterations 1.1955847E-03 2.6371002E-02 at 170iterations 7.3959935E-04 1.8058300E-02 at 180iterations finished qdiffx linear iterations at : 19:03:58 total time elapsed so far: 20.77000 # loops : 180 mean,max change (kT/e) : 7.3959935E-04 1.8058300E-02 energy calculations done at 20.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.01000 DelPhi exited at 19:03:58 21.019u 0.457s 0:22.03 97.4% 0+0k 0+0io 0pf+0w