Mon Oct 10 19:41:47 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 19:41:47 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5094958 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): -18.29200 36.71500 ymin,ymax (A): -30.54000 31.77100 zmin,zma (A): -4.098000 65.77500 x,y,z range (A): 55.00700 62.31100 69.87300 scale (grids/A): 0.5094958 object centre (A): 9.211500 0.6154995 30.83850 number of atom coordinates read : 4641 total number of charged atoms : 4434 net assigned charge : 4.806034 assigned positive charge : 698.7606 centred at (gu) : 90.31538 90.78564 88.26527 assigned negative charge : -693.9590 centred at (gu) : 90.21315 90.85822 88.29541 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7654 nv = 96 ne = 84 npr = 93036 no. pairs analyzed = 93036 no. exposed pairs = 6020 no. arc points = 41853 no. surface atoms = 2012 nbur = 2629 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 = 1.680000 m= 285 mr = 3897 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4103 ## 614 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10305 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1538167E-10 -4.4552877E-12 midg,1,midg; midg,igrid,midg 1.9193343E-10 -1.3837363E-10 1,midg,midg; igrid,midg,midg -1.6891535E-10 3.3220349E-10 gauss-seidel spectral radius is 0.9802934 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 19:41:48 rms-change max change #iterations 6.7096986E-02 12.53483 at 10iterations 3.7589779E-03 0.5781097 at 20iterations 3.0300010E-04 4.3715954E-02 at 30iterations 7.9008765E-05 1.1754274E-02 at 40iterations 3.0064864E-05 4.4438839E-03 at 50iterations finished qdiffx linear iterations at : 19:41:51 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.0064864E-05 4.4438839E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 19:41:51 3.462u 0.195s 0:03.99 91.4% 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 19:41:51 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.528487 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): -18.29200 36.71500 ymin,ymax (A): -30.54000 31.77100 zmin,zma (A): -4.098000 65.77500 x,y,z range (A): 55.00700 62.31100 69.87300 scale (grids/A): 1.528487 object centre (A): 9.211500 0.6154995 30.83850 number of atom coordinates read : 4641 total number of charged atoms : 4434 net assigned charge : 4.806034 assigned positive charge : 698.7606 centred at (gu) : 90.94471 92.35555 84.79442 assigned negative charge : -693.9590 centred at (gu) : 90.63931 92.57434 84.88602 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 86516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25128 mr = 58776 m= 2164 mr = 16628 m= 50 mr = 914 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 607 time to turn everything in is 0.6100000 number of dielectric boundary points 37538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 33353 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) : 0.5094958 object centre at (A) : 9.211500 0.6154995 30.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5499011E-03 -2.8824019E-03 midg,1,midg; midg,igrid,midg 6.7282822E-03 -1.2855936E-02 1,midg,midg; igrid,midg,midg -1.6138077E-03 1.1966661E-02 gauss-seidel spectral radius is 0.9980955 estimated iterations to convergence 182 setup time was (sec) 0.9000000 now iterating at: 19:41:52 rms-change max change #iterations 3.727827 192.9349 at 10iterations 1.513831 51.33537 at 20iterations 0.6203215 20.02207 at 30iterations 0.2528706 7.788101 at 40iterations 0.1034382 3.254537 at 50iterations 4.2304996E-02 1.434433 at 60iterations 1.7299477E-02 0.5417142 at 70iterations 7.0818062E-03 0.2518921 at 80iterations 2.9187265E-03 0.1073875 at 90iterations 1.2081283E-03 3.9560318E-02 at 100iterations 5.1216903E-04 1.8302917E-02 at 110iterations 2.2924913E-04 7.5088739E-03 at 120iterations finished qdiffx linear iterations at : 19:41:59 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 2.2924913E-04 7.5088739E-03 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 19:42:00 7.619u 0.222s 0:08.20 95.4% 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 19:42:00 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.292731 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): -18.29200 36.71500 ymin,ymax (A): -30.54000 31.77100 zmin,zma (A): -4.098000 65.77500 x,y,z range (A): 55.00700 62.31100 69.87300 scale (grids/A): 2.292731 object centre (A): 9.211500 0.6154995 30.83850 number of atom coordinates read : 4641 total number of charged atoms : 4434 net assigned charge : 4.806034 assigned positive charge : 698.7606 centred at (gu) : 91.41664 93.53313 82.19131 assigned negative charge : -693.9590 centred at (gu) : 90.95891 93.86146 82.32890 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 201625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 89910 mr = 144664 m= 22750 mr = 69988 m= 3099 mr = 16238 m= 122 mr = 1865 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8299999 no. cavity mid-points inaccessible to solvent = 2037 time to turn everything in is 1.460000 number of dielectric boundary points 84730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 35386 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) : 1.528487 object centre at (A) : 9.211500 0.6154995 30.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1421395 -0.1358328 midg,1,midg; midg,igrid,midg 6.0795113E-02 -0.3063892 1,midg,midg; igrid,midg,midg -2.5445156E-02 0.1809591 gauss-seidel spectral radius is 0.9991564 estimated iterations to convergence 272 setup time was (sec) 1.760000 now iterating at: 19:42:02 rms-change max change #iterations 10.14359 300.3721 at 10iterations 5.816685 153.3024 at 20iterations 3.314740 76.83754 at 30iterations 1.872557 48.78049 at 40iterations 1.056309 24.22696 at 50iterations 0.5925566 13.80956 at 60iterations 0.3324732 6.614307 at 70iterations 0.1853366 3.897125 at 80iterations 0.1035312 2.236368 at 90iterations 5.7586201E-02 1.206054 at 100iterations 3.2032277E-02 0.6666985 at 110iterations 1.7807979E-02 0.3557749 at 120iterations 9.8975822E-03 0.2053778 at 130iterations 5.5098324E-03 0.1148028 at 140iterations 3.0693181E-03 6.7565918E-02 at 150iterations 1.7162492E-03 3.4320831E-02 at 160iterations 9.6439244E-04 2.0101547E-02 at 170iterations 5.5059243E-04 1.1445999E-02 at 180iterations finished qdiffx linear iterations at : 19:42:12 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 5.5059243E-04 1.1445999E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 19:42:13 12.588u 0.255s 0:13.14 97.6% 0+0k 0+0io 0pf+0w