Sat Oct 8 21:51:58 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 Sat Oct 8 2011 at 21:51:58 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 0.5030807 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): -81.32300 -11.02800 ymin,ymax (A): -16.68100 41.18500 zmin,zma (A): -57.15600 13.60800 x,y,z range (A): 70.29500 57.86600 70.76400 scale (grids/A): 0.5030807 object centre (A): -46.17550 12.25200 -21.77400 number of atom coordinates read : 4244 total number of charged atoms : 4085 net assigned charge : 14.00002 assigned positive charge : 644.9311 centred at (gu) : 89.34961 91.61746 90.26493 assigned negative charge : -630.9343 centred at (gu) : 89.35252 91.57703 90.22430 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6949 nv = 96 ne = 84 npr = 82199 no. pairs analyzed = 82199 no. exposed pairs = 5652 no. arc points = 40517 no. surface atoms = 1892 nbur = 2352 mkacc time = 0.1800000 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 = 1.708000 m= 250 mr = 3286 m= 0 mr = 9 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4005 ## 652 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9302 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7481229E-11 2.2093503E-10 midg,1,midg; midg,igrid,midg 4.8594101E-11 3.1623176E-10 1,midg,midg; igrid,midg,midg 1.7087103E-10 1.1382057E-10 gauss-seidel spectral radius is 0.9797698 estimated iterations to convergence 58 setup time was (sec) 0.6400000 now iterating at: 21:51:59 rms-change max change #iterations 5.7617202E-02 10.97452 at 10iterations 3.5768452E-03 0.6586113 at 20iterations 4.5305138E-04 8.6563110E-02 at 30iterations 1.0697326E-04 1.9208908E-02 at 40iterations 2.7676235E-05 5.0163269E-03 at 50iterations finished qdiffx linear iterations at : 21:52:02 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.7676235E-05 5.0163269E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 21:52:02 3.302u 0.147s 0:03.75 91.7% 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 8 2011 at 21:52:02 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 1.509242 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): -81.32300 -11.02800 ymin,ymax (A): -16.68100 41.18500 zmin,zma (A): -57.15600 13.60800 x,y,z range (A): 70.29500 57.86600 70.76400 scale (grids/A): 1.509242 object centre (A): -46.17550 12.25200 -21.77400 number of atom coordinates read : 4244 total number of charged atoms : 4085 net assigned charge : 14.00002 assigned positive charge : 644.9311 centred at (gu) : 88.04725 94.85139 90.79364 assigned negative charge : -630.9343 centred at (gu) : 88.05688 94.73050 90.67242 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40517 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 22451 mr = 50881 m= 2099 mr = 14213 m= 32 mr = 900 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 36545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 571 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 30489 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) : 0.5030807 object centre at (A) : -46.17550 12.25200 -21.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0783549E-03 2.1237627E-02 midg,1,midg; midg,igrid,midg 4.9434127E-03 1.5018729E-02 1,midg,midg; igrid,midg,midg 1.4291130E-04 -1.7900624E-03 gauss-seidel spectral radius is 0.9979924 estimated iterations to convergence 177 setup time was (sec) 0.8600000 now iterating at: 21:52:03 rms-change max change #iterations 3.400978 163.4853 at 10iterations 1.342940 48.22296 at 20iterations 0.5358927 19.58604 at 30iterations 0.2122332 7.968590 at 40iterations 8.5046500E-02 3.717254 at 50iterations 3.3850338E-02 1.129674 at 60iterations 1.3520472E-02 0.5037667 at 70iterations 5.3997659E-03 0.2024403 at 80iterations 2.1799360E-03 8.0375671E-02 at 90iterations 8.8466646E-04 3.0309677E-02 at 100iterations 3.6954781E-04 1.2790680E-02 at 110iterations 1.6197751E-04 6.2456131E-03 at 120iterations finished qdiffx linear iterations at : 21:52:11 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 1.6197751E-04 6.2456131E-03 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 21:52:11 8.457u 0.193s 0:08.97 96.3% 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 8 2011 at 21:52:11 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 2.263863 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): -81.32300 -11.02800 ymin,ymax (A): -16.68100 41.18500 zmin,zma (A): -57.15600 13.60800 x,y,z range (A): 70.29500 57.86600 70.76400 scale (grids/A): 2.263863 object centre (A): -46.17550 12.25200 -21.77400 number of atom coordinates read : 4244 total number of charged atoms : 4085 net assigned charge : 14.00002 assigned positive charge : 644.9311 centred at (gu) : 87.07043 97.27686 91.19014 assigned negative charge : -630.9343 centred at (gu) : 87.08528 97.09566 91.00855 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 181462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40517 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 79713 mr = 126117 m= 20430 mr = 60048 m= 2956 mr = 14250 m= 124 mr = 1782 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 82465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 32558 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) : 1.509242 object centre at (A) : -46.17550 12.25200 -21.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1511641 0.5115231 midg,1,midg; midg,igrid,midg 5.4011535E-02 0.1916626 1,midg,midg; igrid,midg,midg 6.7853659E-02 -0.4567683 gauss-seidel spectral radius is 0.9991121 estimated iterations to convergence 265 setup time was (sec) 1.610000 now iterating at: 21:52:13 rms-change max change #iterations 9.405140 267.4826 at 10iterations 5.323884 142.3741 at 20iterations 2.986214 74.48756 at 30iterations 1.663373 46.06744 at 40iterations 0.9211103 22.78152 at 50iterations 0.5077227 10.67117 at 60iterations 0.2800374 6.512965 at 70iterations 0.1537214 3.240051 at 80iterations 8.4338158E-02 1.674566 at 90iterations 4.6134073E-02 0.9335175 at 100iterations 2.5248198E-02 0.5095978 at 110iterations 1.3761883E-02 0.2876854 at 120iterations 7.5240815E-03 0.1471252 at 130iterations 4.1088532E-03 7.9759598E-02 at 140iterations 2.2422289E-03 4.5248508E-02 at 150iterations 1.2225191E-03 2.4948120E-02 at 160iterations 6.6675775E-04 1.3377905E-02 at 170iterations 3.6447943E-04 7.2631836E-03 at 180iterations finished qdiffx linear iterations at : 21:52:23 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 3.6447943E-04 7.2631836E-03 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 21:52:24 12.263u 0.232s 0:12.77 97.8% 0+0k 0+0io 0pf+0w